Dasytricha dominance in Surti buffalo rumen revealed by 18S rRNA sequences and real-time PCR assay.

PubMed

Singh, K M; Tripathi, A K; Pandya, P R; Rank, D N; Kothari, R K; Joshi, C G

2011-09-01

The genetic diversity of protozoa in Surti buffalo rumen was studied by amplified ribosomal DNA restriction analysis, 18S rDNA sequence homology and phylogenetic and Real-time PCR analysis methods. Three animals were fed diet comprised green fodder Napier bajra 21 (Pennisetum purpureum), mature pasture grass (Dicanthium annulatum) and concentrate mixture (20% crude protein, 65% total digestible nutrients). A protozoa-specific primer (P-SSU-342f) and a eukarya-specific primer (Medlin B) were used to amplify a 1,360 bp fragment of DNA encoding protozoal small subunit (SSU) ribosomal RNA from rumen fluid. A total of 91 clones were examined and identified 14 different 18S RNA sequences based on PCR-RFLP pattern. These 14 phylotypes were distributed into four genera-based 18S rDNA database sequences and identified as Dasytricha (57 clones), Isotricha (14 clones), Ostracodinium (11 clones) and Polyplastron (9 clones). Phylogenetic analyses were also used to infer the makeup of protozoa communities in the rumen of Surti buffalo. Out of 14 sequences, 8 sequences (69 clones) clustered with the Dasytricha ruminantium-like clone and 4 sequences (13 clones) were also phylogenetically placed with the Isotricha prostoma-like clone. Moreover, 2 phylotypes (9 clones) were related to Polyplastron multivesiculatum-like clone. In addition, the number of 18S rDNA gene copies of Dasytricha ruminantium (0.05% to ciliate protozoa) was higher than Entodinium sp. (2.0 × 10(5) vs. 1.3 × 10(4)) in per ml ruminal fluid.

Analytical Performances of Human Immunodeficiency Virus Type 1 RNA-Based Amplix® Real-Time PCR Platform for HIV-1 RNA Quantification

PubMed Central

Mboumba Bouassa, Ralph-Sydney; Jenabian, Mohammad-Ali; Wolyec, Serge Tonen; Robin, Leman; Matta, Mathieu; Longo, Jean de Dieu; Grésenguet, Gérard; Andreoletti, Laurent; Bélec, Laurent

2016-01-01

Objectives. We evaluated the performances of Amplix real-time PCR platform developed by Biosynex (Strasbourg, France), combining automated station extraction (Amplix station 16 Dx) and real-time PCR (Amplix NG), for quantifying plasma HIV-1 RNA by lyophilized HIV-1 RNA-based Amplix reagents targeting gag and LTR, using samples from HIV-1-infected adults from Central African Republic. Results. Amplix real-time PCR assay showed low limit of detection (28 copies/mL), across wide dynamic range (1.4–10 log copies/mL), 100% sensitivity and 99% specificity, high reproducibility, and accuracy with mean bias < 5%. The assay showed excellent correlations and concordance of 95.3% with the reference HIV-1 RNA load assay (Roche), with mean absolute bias of +0.097 log copies/mL by Bland-Altman analysis. The assay was able to detect and quantify the most prevalent HIV-1 subtype strains and the majority of non-B subtypes, CRFs of HIV-1 group M, and HIV-1 groups N and O circulating in Central Africa. The Amplix assay showed 100% sensitivity and 99.6% specificity to diagnose virological failure in clinical samples from antiretroviral drug-experienced patients. Conclusions. The HIV-1 RNA-based Amplix real-time PCR platform constitutes sensitive and reliable system for clinical monitoring of HIV-1 RNA load in HIV-1-infected children and adults, particularly adapted to intermediate laboratory facilities in sub-Saharan Africa. PMID:28050283

A Metrics-Based Approach to Intrusion Detection System Evaluation for Distributed Real-Time Systems

DTIC Science & Technology

2002-04-01

Based Approach to Intrusion Detection System Evaluation for Distributed Real - Time Systems Authors: G. A. Fink, B. L. Chappell, T. G. Turner, and...Distributed, Security. 1 Introduction Processing and cost requirements are driving future naval combat platforms to use distributed, real - time systems of...distributed, real - time systems . As these systems grow more complex, the timing requirements do not diminish; indeed, they may become more constrained

Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines.

PubMed

Oliveira, Francisco P M; Tavares, João Manuel R S

2013-03-01

This article presents an enhanced methodology to align plantar pressure image sequences simultaneously in time and space. The temporal alignment of the sequences is accomplished using B-splines in the time modeling, and the spatial alignment can be attained using several geometric transformation models. The methodology was tested on a dataset of 156 real plantar pressure image sequences (3 sequences for each foot of the 26 subjects) that was acquired using a common commercial plate during barefoot walking. In the alignment of image sequences that were synthetically deformed both in time and space, an outstanding accuracy was achieved with the cubic B-splines. This accuracy was significantly better (p < 0.001) than the one obtained using the best solution proposed in our previous work. When applied to align real image sequences with unknown transformation involved, the alignment based on cubic B-splines also achieved superior results than our previous methodology (p < 0.001). The consequences of the temporal alignment on the dynamic center of pressure (COP) displacement was also assessed by computing the intraclass correlation coefficients (ICC) before and after the temporal alignment of the three image sequence trials of each foot of the associated subject at six time instants. The results showed that, generally, the ICCs related to the medio-lateral COP displacement were greater when the sequences were temporally aligned than the ICCs of the original sequences. Based on the experimental findings, one can conclude that the cubic B-splines are a remarkable solution for the temporal alignment of plantar pressure image sequences. These findings also show that the temporal alignment can increase the consistency of the COP displacement on related acquired plantar pressure image sequences.

Real-time tricolor phase measuring profilometry based on CCD sensitivity calibration

NASA Astrophysics Data System (ADS)

Zhu, Lin; Cao, Yiping; He, Dawu; Chen, Cheng

2017-02-01

A real-time tricolor phase measuring profilometry (RTPMP) based on charge coupled device (CCD) sensitivity calibration is proposed. Only one colour fringe pattern whose red (R), green (G) and blue (B) components are, respectively, coded as three sinusoidal phase-shifting gratings with an equivalent shifting phase of 2π/3 is needed and sent to an appointed flash memory on a specialized digital light projector (SDLP). A specialized time-division multiplexing timing sequence actively controls the SDLP to project the fringe patterns in R, G and B channels sequentially onto the measured object in one over seventy-two of a second and meanwhile actively controls a high frame rate monochrome CCD camera to capture the corresponding deformed patterns synchronously with the SDLP. So the sufficient information for reconstructing the three-dimensional (3D) shape in one over twenty-four of a second is obtained. Due to the different spectral sensitivity of the CCD camera to RGB lights, the captured deformed patterns from R, G and B channels cannot share the same peak and valley, which will lead to lower accuracy or even failing to reconstruct the 3D shape. So a deformed pattern amending method based on CCD sensitivity calibration is developed to guarantee the accurate 3D reconstruction. The experimental results verify the feasibility of the proposed RTPMP method. The proposed RTPMP method can obtain the 3D shape at over the video frame rate of 24 frames per second, avoid the colour crosstalk completely and be effective for measuring real-time changing object.

Approaching near real-time biosensing: microfluidic microsphere based biosensor for real-time analyte detection.

PubMed

Cohen, Noa; Sabhachandani, Pooja; Golberg, Alexander; Konry, Tania

2015-04-15

In this study we describe a simple lab-on-a-chip (LOC) biosensor approach utilizing well mixed microfluidic device and a microsphere-based assay capable of performing near real-time diagnostics of clinically relevant analytes such cytokines and antibodies. We were able to overcome the adsorption kinetics reaction rate-limiting mechanism, which is diffusion-controlled in standard immunoassays, by introducing the microsphere-based assay into well-mixed yet simple microfluidic device with turbulent flow profiles in the reaction regions. The integrated microsphere-based LOC device performs dynamic detection of the analyte in minimal amount of biological specimen by continuously sampling micro-liter volumes of sample per minute to detect dynamic changes in target analyte concentration. Furthermore we developed a mathematical model for the well-mixed reaction to describe the near real time detection mechanism observed in the developed LOC method. To demonstrate the specificity and sensitivity of the developed real time monitoring LOC approach, we applied the device for clinically relevant analytes: Tumor Necrosis Factor (TNF)-α cytokine and its clinically used inhibitor, anti-TNF-α antibody. Based on the reported results herein, the developed LOC device provides continuous sensitive and specific near real-time monitoring method for analytes such as cytokines and antibodies, reduces reagent volumes by nearly three orders of magnitude as well as eliminates the washing steps required by standard immunoassays. Copyright © 2014 Elsevier B.V. All rights reserved.

Constructing and Modifying Sequence Statistics for relevent Using informR in &#x1D5B1;

PubMed Central

Marcum, Christopher Steven; Butts, Carter T.

2015-01-01

The informR package greatly simplifies the analysis of complex event histories in &#x1D5B1; by providing user friendly tools to build sufficient statistics for the relevent package. Historically, building sufficient statistics to model event sequences (of the form a→b) using the egocentric generalization of Butts’ (2008) relational event framework for modeling social action has been cumbersome. The informR package simplifies the construction of the complex list of arrays needed by the rem() model fitting for a variety of cases involving egocentric event data, multiple event types, and/or support constraints. This paper introduces these tools using examples from real data extracted from the American Time Use Survey. PMID:26185488

CNR considerations for rapid real-time MRI tumor tracking in radiotherapy hybrid devices: Effects of B{sub 0} field strength

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wachowicz, K., E-mail: keith.wachowicz@albertaheal

2016-08-15

Purpose: This work examines the subject of contrast-to-noise ratio (CNR), specifically between tumor and tissue background, and its dependence on the MRI field strength, B{sub 0}. This examination is motivated by the recent interest and developments in MRI/radiotherapy hybrids where real-time imaging can be used to guide treatment beams. The ability to distinguish a tumor from background tissue is of primary importance in this field, and this work seeks to elucidate the complex relationship between the CNR and B{sub 0} that is too often assumed to be purely linear. Methods: Experimentally based models of B{sub 0}-dependant relaxation for various tumormore » and normal tissues from the literature were used in conjunction with signal equations for MR sequences suitable for rapid real-time imaging to develop field-dependent predictions for CNR. These CNR models were developed for liver, lung, breast, glioma, and kidney tumors for spoiled gradient-echo, balanced steady-state free precession (bSSFP), and single-shot half-Fourier fast spin echo sequences. Results: Due to the pattern in which the relaxation properties of tissues are found to vary over B{sub 0} field (specifically the T{sub 1} time), there was always an improved CNR at lower fields compared to linear dependency. Further, in some tumor sites, the CNR at lower fields was found to be comparable to, or sometimes higher than those at higher fields (i.e., bSSFP CNR for glioma, kidney, and liver tumors). Conclusions: In terms of CNR, lower B{sub 0} fields have been shown to perform as well or better than higher fields for some tumor sites due to superior T{sub 1} contrast. In other sites this effect was less pronounced, reversing the CNR advantage. This complex relationship between CNR and B{sub 0} reveals both low and high magnetic fields as viable options for tumor tracking in MRI/radiotherapy hybrids.« less

VEST: An Aspect-Based Composition Tool for Real-Time Systems

DTIC Science & Technology

2003-01-01

VEST: An Aspect-Based Composition Tool for Real - Time Systems * John A. Stankovic Ruiqing Zhu Ram Poornalingam Chenyang Lu Zhendong Yu Marty Humphrey...Composition Tool for Real - Time Systems 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK...it is obvious that designers of embedded real - time systems face many difficult problems. By working through various product scenarios with avionics

BMPR1B mutation causes Pierre Robin sequence

PubMed Central

Yao, Xu; Zhang, Rong; Yang, Hui; Zhao, Rui; Guo, Jihong; Jin, Ke; Mei, Haibo; Luo, Yongqi; Zhao, Liu; Tu, Ming; Zhu, Yimin

2017-01-01

Background We investigated a large family with Pierre Robin sequence (PRS). Aim of the study This study aims to determine the genetic cause of PRS. Results The reciprocal translocation t(4;6)(q22;p21) was identified to be segregated with PRS in a three-generation family. Whole-genome sequencing and Sanger sequencing successfully detected breakpoints in the intragenic regions of BMRP1B and GRM4. We hypothesized that PRS in this family was caused by (i) haploinsufficiency for BMPR1B or (ii) a gain of function mechanism mediated by the BMPR1B-GRM4 fusion gene. In an unrelated family, we identified another BMPR1B-splicing mutation that co-segregated with PRS. Conclusion We detected two BMPR1B mutations in two unrelated PRS families, suggesting that BMPR1B disruption is probably a cause of human PRS. Methods GTG banding, comparative genomic hybridization, whole-genome sequencing, and Sanger sequencing were performed to identify the gene causing PRS. PMID:28418932

Evaluation of the Abbott Real Time HCV genotype II assay for Hepatitis C virus genotyping.

PubMed

Sariguzel, Fatma Mutlu; Berk, Elife; Gokahmetoglu, Selma; Ercal, Baris Derya; Celik, Ilhami

2015-01-01

The determination of HCV genotypes and subtypes is very important for the selection of antiviral therapy and epidemiological studies. The aim of this study was to evaluate the performance of Abbott Real Time HCV Genotype II assay in HCV genotyping of HCV infected patients in Kayseri, Turkey. One hundred patients with chronic hepatitis C admitted to our hospital were evaluated between June 2012 and December 2012, HCV RNA levels were determined by the COBAS® AmpliPrep/COBAS® TaqMan® 48 HCV test. HCV genotyping was investigated by the Abbott Real Time HCV Genotype II assay. With the exception of genotype 1, subtypes of HCV genotypes could not be determined by Abbott assay. Sequencing analysis was used as the reference method. Genotypes 1, 2, 3 and 4 were observed in 70, 4, 2 and 24 of the 100 patients, respectively, by two methods. The concordance between the two systems to determine HCV major genotypes was 100%. Of 70 patients with genotype 1, 66 showed infection with subtype 1b and 4 with subtype 1a by Abbott Real Time HCV Genotype II assay. Using sequence analysis, 61 showed infection with subtype 1b and 9 with subtype 1a. In determining of HCV genotype 1 subtypes, the difference between the two methods was not statistically significant (P>0.05). HCV genotype 4 and 3 samples were found to be subtype 4d and 3a, respectively, by sequence analysis. There were four patients with genotype 2. Sequence analysis revealed that two of these patients had type 2a and the other two had type 2b. The Abbott Real Time HCV Genotype II assay yielded results consistent with sequence analysis. However, further optimization of the Abbott Real Time HCV Genotype II assay for subtype identification of HCV is required.

A Quadruplex Real-Time PCR Assay for the Rapid Detection and Differentiation of the Most Relevant Members of the B. pseudomallei Complex: B. mallei, B. pseudomallei, and B. thailandensis

PubMed Central

Lowe, Chinn-Woan; Thiriot, Joseph D.; Heder, Michael J.; March, Jordon K.; Drake, David S.; Lew, Cynthia S.; Bunnell, Annette J.; Moore, Emily S.; O'Neill, Kim L.; Robison, Richard A.

2016-01-01

The Burkholderia pseudomallei complex classically consisted of B. mallei, B. pseudomallei, and B. thailandensis, but has now expanded to include B. oklahomensis, B. humptydooensis, and three unassigned Burkholderia clades. Methods for detecting and differentiating the B. pseudomallei complex has been the topic of recent research due to phenotypic and genotypic similarities of these species. B. mallei and B. pseudomallei are recognized as CDC Tier 1 select agents, and are the causative agents of glanders and melioidosis, respectively. Although B. thailandensis and B. oklahomensis are generally avirulent, both display similar phenotypic characteristics to that of B. pseudomallei. B. humptydooensis and the Burkholderia clades are genetically similar to the B. pseudomallei complex, and are not associated with disease. Optimal identification of these species remains problematic, and PCR-based methods can resolve issues with B. pseudomallei complex detection and differentiation. Currently, no PCR assay is available that detects the major species of the B. pseudomallei complex. A real-time PCR assay in a multiplex single-tube format was developed to simultaneously detect and differentiate B. mallei, B. pseudomallei, and B. thailandensis, and a common sequence found in B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis. A total of 309 Burkholderia isolates and 5 other bacterial species were evaluated. The assay was 100% sensitive and specific, demonstrated sensitivity beyond culture and GC methods for the isolates tested, and is completed in about an hour with a detection limit between 2.6pg and 48.9pg of gDNA. Bioinformatic analyses also showed the assay is likely 100% specific and sensitive for all 84 fully sequenced B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis strains currently available in GenBank. For these reasons, this assay could be a rapid and sensitive tool in the detection and differentiation for those species of the B

A Quadruplex Real-Time PCR Assay for the Rapid Detection and Differentiation of the Most Relevant Members of the B. pseudomallei Complex: B. mallei, B. pseudomallei, and B. thailandensis.

PubMed

Lowe, Chinn-Woan; Satterfield, Benjamin A; Nelson, Daniel B; Thiriot, Joseph D; Heder, Michael J; March, Jordon K; Drake, David S; Lew, Cynthia S; Bunnell, Annette J; Moore, Emily S; O'Neill, Kim L; Robison, Richard A

2016-01-01

The Burkholderia pseudomallei complex classically consisted of B. mallei, B. pseudomallei, and B. thailandensis, but has now expanded to include B. oklahomensis, B. humptydooensis, and three unassigned Burkholderia clades. Methods for detecting and differentiating the B. pseudomallei complex has been the topic of recent research due to phenotypic and genotypic similarities of these species. B. mallei and B. pseudomallei are recognized as CDC Tier 1 select agents, and are the causative agents of glanders and melioidosis, respectively. Although B. thailandensis and B. oklahomensis are generally avirulent, both display similar phenotypic characteristics to that of B. pseudomallei. B. humptydooensis and the Burkholderia clades are genetically similar to the B. pseudomallei complex, and are not associated with disease. Optimal identification of these species remains problematic, and PCR-based methods can resolve issues with B. pseudomallei complex detection and differentiation. Currently, no PCR assay is available that detects the major species of the B. pseudomallei complex. A real-time PCR assay in a multiplex single-tube format was developed to simultaneously detect and differentiate B. mallei, B. pseudomallei, and B. thailandensis, and a common sequence found in B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis. A total of 309 Burkholderia isolates and 5 other bacterial species were evaluated. The assay was 100% sensitive and specific, demonstrated sensitivity beyond culture and GC methods for the isolates tested, and is completed in about an hour with a detection limit between 2.6pg and 48.9pg of gDNA. Bioinformatic analyses also showed the assay is likely 100% specific and sensitive for all 84 fully sequenced B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis strains currently available in GenBank. For these reasons, this assay could be a rapid and sensitive tool in the detection and differentiation for those species of the B

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

PubMed Central

Ardui, Simon; Ameur, Adam; Vermeesch, Joris R; Hestand, Matthew S

2018-01-01

Abstract Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems. Here we capsulize how SMRT sequencing is revolutionizing constitutional, reproductive, cancer, microbial and viral genetic testing. PMID:29401301

Open-circuit respirometry: real-time, laboratory-based systems.

PubMed

Ward, Susan A

2018-05-04

This review explores the conceptual and technological factors integral to the development of laboratory-based, automated real-time open-circuit mixing-chamber and breath-by-breath (B × B) gas-exchange systems, together with considerations of assumptions and limitations. Advances in sensor technology, signal analysis, and digital computation led to the emergence of these technologies in the mid-20th century, at a time when investigators were beginning to recognise the interpretational advantages of nonsteady-state physiological-system interrogation in understanding the aetiology of exercise (in)tolerance in health, sport, and disease. Key milestones include the 'Auchincloss' description of an off-line system to estimate alveolar O 2 uptake B × B during exercise. This was followed by the first descriptions of real-time automated O 2 uptake and CO 2 output B × B measurement by Beaver and colleagues and by Linnarsson and Lindborg, and mixing-chamber measurement by Wilmore and colleagues. Challenges to both approaches soon emerged: e.g., the influence of mixing-chamber washout kinetics on mixed-expired gas concentration determination, and B × B alignment of gas-concentration signals with respired flow. The challenging algorithmic and technical refinements required for gas-exchange estimation at the alveolar level have also been extensively explored. In conclusion, while the technology (both hardware and software) underpinning real-time automated gas-exchange measurement has progressively advanced, there are still concerns regarding accuracy especially under the challenging conditions of changing metabolic rate.

Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time?

PubMed

McGann, Patrick; Bunin, Jessica L; Snesrud, Erik; Singh, Seema; Maybank, Rosslyn; Ong, Ana C; Kwak, Yoon I; Seronello, Scott; Clifford, Robert J; Hinkle, Mary; Yamada, Stephen; Barnhill, Jason; Lesho, Emil

2016-07-01

Whole genome sequencing (WGS) is increasingly employed in clinical settings, though few assessments of turnaround times (TAT) have been performed in real-time. In this study, WGS was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium (VRE) among 3 patients in the ICU of a tertiary care hospital. Including overnight culturing, a TAT of just 48.5 h for a comprehensive report was achievable using an Illumina Miseq benchtop sequencer. WGS revealed that isolates from patient 2 and 3 differed from that of patient 1 by a single nucleotide polymorphism (SNP), indicating nosocomial transmission. However, the unparalleled resolution provided by WGS suggested that nosocomial transmission involved two separate events from patient 1 to patient 2 and 3, and not a linear transmission suspected by the time line. Rapid TAT's are achievable using WGS in the clinical setting and can provide an unprecedented level of resolution for outbreak investigations. Published by Elsevier Inc.

Real-time volumetric relative dosimetry for magnetic resonance—image-guided radiation therapy (MR-IGRT)

NASA Astrophysics Data System (ADS)

Lee, Hannah J.; Kadbi, Mo; Bosco, Gary; Ibbott, Geoffrey S.

2018-02-01

The integration of magnetic resonance imaging (MRI) with linear accelerators (linac) has enabled the use of 3D MR-visible gel dosimeters for real-time verification of volumetric dose distributions. Several iron-based radiochromic 3D gels were created in-house then imaged and irradiated in a pre-clinical 1.5 T-7 MV MR-Linac. MR images were acquired using a range of balanced-fast field echo (b-FFE) sequences during irradiation to assess the contrast and dose response in irradiated regions and to minimize the presence of MR artifacts. Out of four radiochromic 3D gel formulations, the FOX 3D gel was found to provide superior MR contrast in the irradiated regions. The FOX gels responded linearly with respect to real-time dose and the signal remained stable post-irradiation for at least 20 min. The response of the FOX gel also was found to be unaffected by the radiofrequency and gradient fields created by the b-FFE sequence during irradiation. A reusable version of the FOX gel was used for b-FFE sequence optimization to reduce artifacts by increasing the number of averages at the expense of temporal resolution. Regardless of the real-time MR sequence used, the FOX 3D gels responded linearly to dose with minimal magnetic field effects due to the strong 1.5 T field or gradient fields present during imaging. These gels can easily be made in-house using non-reusable and reusable formulations depending on the needs of the clinic, and the results of this study encourage further applications of 3D gels for MR-IGRT applications.

Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

PubMed Central

Scheutz, Flemming; Lund, Ole; Hasman, Henrik; Kaas, Rolf S.; Nielsen, Eva M.; Aarestrup, Frank M.

2014-01-01

Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all suspected VTEC isolates. During a 7-week period in the fall of 2012, all incoming isolates were concurrently subjected to WGS using IonTorrent PGM. Real-time bioinformatics analysis was performed using web-tools (www.genomicepidemiology.org) for species determination, multilocus sequence type (MLST) typing, and determination of phylogenetic relationship, and a specific VirulenceFinder for detection of E. coli virulence genes was developed as part of this study. In total, 46 suspected VTEC isolates were characterized in parallel during the study. VirulenceFinder proved successful in detecting virulence genes included in routine typing, explicitly verocytotoxin 1 (vtx1), verocytotoxin 2 (vtx2), and intimin (eae), and also detected additional virulence genes. VirulenceFinder is also a robust method for assigning verocytotoxin (vtx) subtypes. A real-time clustering of isolates in agreement with the epidemiology was established from WGS, enabling discrimination between sporadic and outbreak isolates. Overall, WGS typing produced results faster and at a lower cost than the current routine. Therefore, WGS typing is a superior alternative to conventional typing strategies. This approach may also be applied to typing and surveillance of other pathogens. PMID:24574290

Development of a real-time PCR for detection of Staphylococcus pseudintermedius using a novel automated comparison of whole-genome sequences.

PubMed

Verstappen, Koen M; Huijbregts, Loes; Spaninks, Mirlin; Wagenaar, Jaap A; Fluit, Ad C; Duim, Birgitta

2017-01-01

Staphylococcus pseudintermedius is an opportunistic pathogen in dogs and cats and occasionally causes infections in humans. S. pseudintermedius is often resistant to multiple classes of antimicrobials. It requires a reliable detection so that it is not misidentified as S. aureus. Phenotypic and currently-used molecular-based diagnostic assays lack specificity or are labour-intensive using multiplex PCR or nucleic acid sequencing. The aim of this study was to identify a specific target for real-time PCR by comparing whole genome sequences of S. pseudintermedius and non-pseudintermedius.Genome sequences were downloaded from public repositories and supplemented by isolates that were sequenced in this study. A Perl-script was written that analysed 300-nt fragments from a reference genome sequence of S. pseudintermedius and checked if this sequence was present in other S. pseudintermedius genomes (n = 74) and non-pseudintermedius genomes (n = 138). Six sequences specific for S. pseudintermedius were identified (sequence length between 300-500 nt). One sequence, which was located in the spsJ gene, was used to develop primers and a probe. The real-time PCR showed 100% specificity when testing for S. pseudintermedius isolates (n = 54), and eight other staphylococcal species (n = 43). In conclusion, a novel approach by comparing whole genome sequences identified a sequence that is specific for S. pseudintermedius and provided a real-time PCR target for rapid and reliable detection of S. pseudintermedius.

Development of real-time PCR assay for genetic identification of the mottled skate, Beringraja pulchra.

PubMed

Hwang, In Kwan; Lee, Hae Young; Kim, Min-Hee; Jo, Hyun-Su; Choi, Dong-Ho; Kang, Pil-Won; Lee, Yang-Han; Cho, Nam-Soo; Park, Ki-Won; Chae, Ho Zoon

2015-10-01

The mottled skate, Beringraja pulchra is one of the commercially important fishes in the market today. However, B. pulchra identification methods have not been well developed. The current study reports a novel real-time PCR method based on TaqMan technology developed for the genetic identification of B. pulchra. The mitochondrial cytochrome oxidase subunit 1 (COI) nucleotide sequences of 29 B. pulchra, 157 skates and rays reported in GenBank DNA database were comparatively analyzed and the COI sequences specific to B. pulchra was identified. Based on this information, a system of specific primers and Minor Groove Binding (MGB) TaqMan probe were designed. The assay successfully discriminated in 29 specimens of B. pulchra and 27 commercial samples with unknown species identity. For B. pulchra DNA, an average Threshold Cycle (Ct) value of 19.1±0.1 was obtained. Among 27 commercial samples, two samples showed average Ct values 19.1±0.0 and 26.7±0.1, respectively and were confirmed to be B. pulchra based on sequencing. The other samples tested showed undetectable or extremely weak signals for the target fragment, which was also consistent with the sequencing results. These results reveal that the method developed is a rapid and efficient tool to identify B. pulchra and might prevent fraud or mislabeling during the distribution of B. pulchra products. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Locked Nucleic Acid Probe-Based Real-Time PCR Assay for the Rapid Detection of Rifampin-Resistant Mycobacterium tuberculosis

PubMed Central

Sun, Chongyun; Li, Chao; Wang, Xiaochen; Liu, Haican; Zhang, Pingping; Zhao, Xiuqin; Wang, Xinrui; Jiang, Yi; Yang, Ruifu; Wan, Kanglin; Zhou, Lei

2015-01-01

Drug-resistant Mycobacterium tuberculosis can be rapidly diagnosed through nucleic acid amplification techniques by analyzing the variations in the associated gene sequences. In the present study, a locked nucleic acid (LNA) probe-based real-time PCR assay was developed to identify the mutations in the rpoB gene associated with rifampin (RFP) resistance in M. tuberculosis. Six LNA probes with the discrimination capability of one-base mismatch were designed to monitor the 23 most frequent rpoB mutations. The target mutations were identified using the probes in a “probe dropout” manner (quantification cycle = 0); thus, the proposed technique exhibited superiority in mutation detection. The LNA probe-based real-time PCR assay was developed in a two-tube format with three LNA probes and one internal amplification control probe in each tube. The assay showed excellent specificity to M. tuberculosis with or without RFP resistance by evaluating 12 strains of common non-tuberculosis mycobacteria. The limit of detection of M. tuberculosis was 10 genomic equivalents (GE)/reaction by further introducing a nested PCR method. In a blind validation of 154 clinical mycobacterium isolates, 142/142 (100%) were correctly detected through the assay. Of these isolates, 88/88 (100%) were determined as RFP susceptible and 52/54 (96.3%) were characterized as RFP resistant. Two unrecognized RFP-resistant strains were sequenced and were found to contain mutations outside the range of the 23 mutation targets. In conclusion, this study established a sensitive, accurate, and low-cost LNA probe-based assay suitable for a four-multiplexing real-time PCR instrument. The proposed method can be used to diagnose RFP-resistant tuberculosis in clinical laboratories. PMID:26599667

Real-time detection of S(1D2) photofragments produced from the 1B2(1Σu+) state of CS2 by vacuum ultraviolet photoelectron imaging using 133 nm probe pulses

NASA Astrophysics Data System (ADS)

Horio, Takuya; Spesyvtsev, Roman; Furumido, Yu; Suzuki, Toshinori

2017-07-01

Ultrafast photodissociation dynamics from the 1B2(1Σu+) state of CS2 are studied by time-resolved photoelectron imaging using the fourth (4ω, 198 nm) and sixth (6ω, 133 nm) harmonics of a femtosecond Ti:sapphire laser. The 1B2 state of CS2 was prepared with the 4ω pulses, and subsequent dynamics were probed using the 6ω vacuum ultraviolet (VUV) pulses. The VUV pulses enabled real-time detection of S(1D2) photofragments, produced via CS2*(1B2(1Σu+)) → CS(X 1Σ+) + S(1D2). The photoionization signal of dissociating CS2*(1B2(1Σu+)) molecules starts to decrease at about 100 fs, while the S(1D2) fragments appear with a finite (ca. 400 fs) delay time after the pump pulse. Also discussed is the configuration interaction of the 1B2(1Σu+) state based on relative photoionization cross-sections to different cationic states.

Advanced Hard Real-Time Operating System, The Maruti Project. Part 1.

DTIC Science & Technology

1997-01-01

REAL - TIME OPERATING SYSTEM , THE MARUTI PROJECT Part 1 of 2 Ashok K. Agrawala Satish K. Tripathi Department of Computer Science University of Maryland...Hard Real - Time Operating System , The Maruti Project DASG-60-92-C-0055 5b. Program Element # 62301E 6. Author(s) 5c. Project # DRPB Ashok K. Agrawala...SdSA94), a real - time operating system developed at the I3nversity of Maryland, and conducted extensive experiments under various task

Real-time image-based B-mode ultrasound image simulation of needles using tensor-product interpolation.

PubMed

Zhu, Mengchen; Salcudean, Septimiu E

2011-07-01

In this paper, we propose an interpolation-based method for simulating rigid needles in B-mode ultrasound images in real time. We parameterize the needle B-mode image as a function of needle position and orientation. We collect needle images under various spatial configurations in a water-tank using a needle guidance robot. Then we use multidimensional tensor-product interpolation to simulate images of needles with arbitrary poses and positions using collected images. After further processing, the interpolated needle and seed images are superimposed on top of phantom or tissue image backgrounds. The similarity between the simulated and the real images is measured using a correlation metric. A comparison is also performed with in vivo images obtained during prostate brachytherapy. Our results, carried out for both the convex (transverse plane) and linear (sagittal/para-sagittal plane) arrays of a trans-rectal transducer indicate that our interpolation method produces good results while requiring modest computing resources. The needle simulation method we present can be extended to the simulation of ultrasound images of other wire-like objects. In particular, we have shown that the proposed approach can be used to simulate brachytherapy seeds.

Evaluation of performance across the dynamic range of the Abbott RealTime HIV-1 assay as compared to VERSANT HIV-1 RNA 3.0 and AMPLICOR HIV-1 MONITOR v1.5 using serial dilutions of 39 group M and O viruses.

PubMed

Swanson, Priscilla; Huang, Shihai; Abravaya, Klara; de Mendoza, Carmen; Soriano, Vincent; Devare, Sushil G; Hackett, John

2007-04-01

Performance of the Abbott m2000 instrument system and the Abbott RealTime HIV-1 assay was evaluated using a panel of 37 group M (subtypes A-D, F, G, CRF01_AE, CRF02_AG and unique recombinant forms) and 2 group O virus isolates. Testing was performed on 273 sample dilutions and compared to VERSANT HIV-1 RNA 3.0 (bDNA) and AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5) test results. RealTime HIV-1, bDNA, and Monitor v1.5 tests quantified 87%, 78%, and 81% of samples, respectively. RealTime HIV-1 detected an additional 31 samples at < 40 copies/mL. For group M, RealTime HIV-1 dilution profiles and viral loads were highly correlated with bDNA and Monitor v1.5 values; 87% and 89% of values were within 0.5 log(10) copies/mL. In contrast, the group O viruses were not detected by Monitor v1.5 and were substantially underquantified by approximately 2 log(10) copies/mL in bDNA relative to the RealTime HIV-1 assay. Sequence analysis revealed that RealTime HIV-1 primer/probe binding sites are highly conserved and exhibit fewer nucleotide mismatches relative to Monitor v1.5. The automated m2000 system and RealTime HIV-1 assay offer the advantages of efficient sample processing and throughput with reduced "hands-on" time while providing improved sensitivity, expanded dynamic range and reliable quantification of genetically diverse HIV-1 strains.

Genotype identification of Math1/LacZ knockout mice based on real-time PCR with SYBR Green I dye.

PubMed

Krizhanovsky, Valery; Golenser, Esther; Ben-Arie, Nissim

2004-07-30

Knockout mice are widely used in all fields of biomedical research. Determining the genotype of every newborn mouse is a tedious task, usually performed by Southern blot hybridization or Polymerase Chain Reaction (PCR). We describe here a quick and simple genotype identification assay based on real-time PCR and SYBR Green I dye, without using fluorescent primers. The discrimination between the wild type and targeted alleles is based on a PCR design that leads to a different melting temperature for each product. The identification of the genotype is obvious immediately after amplification, and no post-PCR manipulations are needed, reducing cost and time. Therefore, while the real-time PCR amplification increases the sensitivity, the fact that the reactions tubes are never opened after amplification, reduces the risk of contamination and eliminates errors, which are common during the repeated handling of dozens of samples from the same mouse line. The protocol we provide was tested on Math1 knockout mice, but is general, and may be utilized for any knockout line and real-time thermocycler, without any further modification, accessories or special reagents. Copyright 2004 Elsevier B.V.

Myelin protein zero gene sequencing diagnoses Charcot-Marie-Tooth Type 1B disease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, Y.; Zhang, H.; Madrid, R.

1994-09-01

Charcot-Marie-Tooth disease (CMT), the most common genetic neuropathy, affects about 1 in 2600 people in Norway and is found worldwide. CMT Type 1 (CMT1) has slow nerve conduction with demyelinated Schwann cells. Autosomal dominant CMT Type 1B (CMT1B) results from mutations in the myelin protein zero gene which directs the synthesis of more than half of all Schwann cell protein. This gene was mapped to the chromosome 1q22-1q23.1 borderline by fluorescence in situ hybridization. The first 7 of 7 reported CMT1B mutations are unique. Thus the most effective means to identify CMT1B mutations in at-risk family members and fetuses ismore » to sequence the entire coding sequence in dominant or sporadic CMT patients without the CMT1A duplication. Of the 19 primers used in 16 pars to uniquely amplify the entire MPZ coding sequence, 6 primer pairs were used to amplify and sequence the 6 exons. The DyeDeoxy Terminator cycle sequencing method used with four different color fluorescent lables was superior to manual sequencing because it sequences more bases unambiguously from extracted genomic DNA samples within 24 hours. This protocol was used to test 28 CMT and Dejerine-Sottas patients without CMT1A gene duplication. Sequencing MPZ gene-specific amplified fragments identified 9 polymorphic sites within the 6 exons that encode the 248 amino acid MPZ protein. The large number of major CMT1B mutations identified by single strand sequencing are being verified by reverse strand sequencing and when possible, by restriction enzyme analysis. This protocol can be used to distringuish CMT1B patients from othre CMT phenotypes and to determine the CMT1B status of relatives both presymptomatically and prenatally.« less

Multiplex, Rapid, and Sensitive Isothermal Detection of Nucleic-Acid Sequence by Endonuclease Restriction-Mediated Real-Time Multiple Cross Displacement Amplification.

PubMed

Wang, Yi; Wang, Yan; Zhang, Lu; Liu, Dongxin; Luo, Lijuan; Li, Hua; Cao, Xiaolong; Liu, Kai; Xu, Jianguo; Ye, Changyun

2016-01-01

We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA), which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5' end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labeled at the 5' end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5' end short sequences and their complementary sequences), which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 min, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here, we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer

PubMed Central

Johnson, Sarah S.; Zaikova, Elena; Goerlitz, David S.; Bai, Yu; Tighe, Scott W.

2017-01-01

The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epidemics. Here, we demonstrate the application of offline DNA sequencing of environmental samples using a hand-held nanopore sequencer in a remote field location: the McMurdo Dry Valleys, Antarctica. Sequencing was performed using a MK1B MinION sequencer from Oxford Nanopore Technologies (ONT; Oxford, United Kingdom) that was equipped with software to operate without internet connectivity. One-direction (1D) genomic libraries were prepared using portable field techniques on DNA isolated from desiccated microbial mats. By adequately insulating the sequencer and laptop, it was possible to run the sequencing protocol for up to 2½ h under arduous conditions. PMID:28337073

Real-time image sequence segmentation using curve evolution

NASA Astrophysics Data System (ADS)

Zhang, Jun; Liu, Weisong

2001-04-01

In this paper, we describe a novel approach to image sequence segmentation and its real-time implementation. This approach uses the 3D structure tensor to produce a more robust frame difference signal and uses curve evolution to extract whole objects. Our algorithm is implemented on a standard PC running the Windows operating system with video capture from a USB camera that is a standard Windows video capture device. Using the Windows standard video I/O functionalities, our segmentation software is highly portable and easy to maintain and upgrade. In its current implementation on a Pentium 400, the system can perform segmentation at 5 frames/sec with a frame resolution of 160 by 120.

Construction Strategy for an Internal Amplification Control for Real-Time Diagnostic Assays Using Nucleic Acid Sequence-Based Amplification: Development and Clinical Application

PubMed Central

Rodríguez-Lázaro, David; D'Agostino, Martin; Pla, Maria; Cook, Nigel

2004-01-01

An important analytical control in molecular amplification-based methods is an internal amplification control (IAC), which should be included in each reaction mixture. An IAC is a nontarget nucleic acid sequence which is coamplified simultaneously with the target sequence. With negative results for the target nucleic acid, the absence of an IAC signal indicates that amplification has failed. A general strategy for the construction of an IAC for inclusion in molecular beacon-based real-time nucleic acid sequence-based amplification (NASBA) assays is presented. Construction proceeds in two phases. In the first phase, a double-stranded DNA molecule that contains nontarget sequences flanked by target sequences complementary to the NASBA primers is produced. At the 5′ end of this DNA molecule is a T7 RNA polymerase binding sequence. In the second phase of construction, RNA transcripts are produced from the DNA by T7 RNA polymerase. This RNA is the IAC; it is amplified by the target NASBA primers and is detected by a molecular beacon probe complementary to the internal nontarget sequences. As a practical example, an IAC for use in an assay for the detection of Mycobacterium avium subsp. paratuberculosis is described, its incorporation and optimization within the assay are detailed, and its application to spiked and natural clinical samples is shown to illustrate the correct interpretation of the diagnostic results. PMID:15583319

Real-time chirp-coded imaging with a programmable ultrasound biomicroscope.

PubMed

Bosisio, Mattéo R; Hasquenoph, Jean-Michel; Sandrin, Laurent; Laugier, Pascal; Bridal, S Lori; Yon, Sylvain

2010-03-01

Ultrasound biomicroscopy (UBM) of mice can provide a testing ground for new imaging strategies. The UBM system presented in this paper facilitates the development of imaging and measurement methods with programmable design, arbitrary waveform coding, broad bandwidth (2-80 MHz), digital filtering, programmable processing, RF data acquisition, multithread/multicore real-time display, and rapid mechanical scanning (1.28, 2.56, and 5.12 micros durations) sequences with matched filter analysis are implemented in real time. Chirp and conventional impulse imaging (31 and 46 MHz center frequencies) of a wire phantom at fast sectorial scanning (0.7 degrees ms(-1), 20 frames/s one-way image rate) are compared. Axial and lateral resolutions at the focus with chirps approach impulse imaging resolutions. Chirps yield 10-15 dB gain in SNR and a 2-3 mm gain in imaging depth. Real-time impulse and chirp-coded imaging (at 10-5 frames/s) are demonstrated in the mouse, in vivo. The system's open structure favors test and implementation of new sequences.

A comparative evaluation between real time Roche COBas TAQMAN 48 HCV and bDNA Bayer Versant HCV 3.0.

PubMed

Giraldi, Cristina; Noto, Alessandra; Tenuta, Robert; Greco, Francesca; Perugini, Daniela; Spadafora, Mario; Bianco, Anna Maria Lo; Savino, Olga; Natale, Alfonso

2006-10-01

The HCV virus is a common human pathogen made of a single stranded RNA genome with 9600nt. This work compared two different commercial methods used for HCV viral load, the bDNA Bayer Versant HCV 3.0 and the RealTime Roche COBAS TaqMan 48 HCV. We compared the reproducibility and linearity of the two methods. Seventy-five plasma samples with genotypes 1 to 4, which represent the population (45% genotype 1; 24% genotype 2; 13% genotype 3; 18% genotype 4) were directly processed with the Versanto method based upon signal amplification; the same samples were first extracted (COBAS Ampliprep - TNAI) and then amplified using RealTime PCR (COBAS TaqMan 48). The results obtained indicate the same performance for both methods if they have genotype 1, but in samples with genotypes 2, 3 and 4 the RealTime PCR Roche method gave an underestimation in respect to the Bayer bDNA assay.

An Alu-based, MGB Eclipse real-time PCR method for quantitation of human DNA in forensic samples.

PubMed

Nicklas, Janice A; Buel, Eric

2005-09-01

The forensic community needs quick, reliable methods to quantitate human DNA in crime scene samples to replace the laborious and imprecise slot blot method. A real-time PCR based method has the possibility of allowing development of a faster and more quantitative assay. Alu sequences are primate-specific and are found in many copies in the human genome, making these sequences an excellent target or marker for human DNA. This paper describes the development of a real-time Alu sequence-based assay using MGB Eclipse primers and probes. The advantages of this assay are simplicity, speed, less hands-on-time and automated quantitation, as well as a large dynamic range (128 ng/microL to 0.5 pg/microL).

Real-time PCR-based method for rapid detection of Aspergillus niger and Aspergillus welwitschiae isolated from coffee.

PubMed

von Hertwig, Aline Morgan; Sant'Ana, Anderson S; Sartori, Daniele; da Silva, Josué José; Nascimento, Maristela S; Iamanaka, Beatriz Thie; Pelegrinelli Fungaro, Maria Helena; Taniwaki, Marta Hiromi

2018-05-01

Some species from Aspergillus section Nigri are morphologically very similar and altogether have been called A. niger aggregate. Although the species included in this group are morphologically very similar, they differ in their ability to produce mycotoxins and other metabolites and their taxonomical status has evolved continuously. Among them, A. niger and A. welwitschiae are ochratoxin A and fumonisin B 2 producers and their detection and/or identification is of crucial importance for food safety. The aim of this study was the development of a real-time PCR-based method for simultaneous discrimination of A. niger and A. welwitschiae from other species of the A. niger aggregate isolated from coffee beans. One primer pair and a hybridization probe specific for detection of A. niger and A. welwitschiae strains were designed based on the BenA gene sequences, and used in a Real-time PCR assay for the rapid discrimination between both these species from all others of the A. niger aggregate. The Real-time PCR assay was shown to be 100% efficient in discriminating the 73 isolates of A. niger/A. welwitschiae from the other A. niger aggregate species analyzed as a negative control. This result testifies to the use of this technique as a good tool in the rapid detection of these important toxigenic species. Copyright © 2018 Elsevier B.V. All rights reserved.

[The principle and application of the single-molecule real-time sequencing technology].

PubMed

Yanhu, Liu; Lu, Wang; Li, Yu

2015-03-01

Last decade witnessed the explosive development of the third-generation sequencing strategy, including single-molecule real-time sequencing (SMRT), true single-molecule sequencing (tSMSTM) and the single-molecule nanopore DNA sequencing. In this review, we summarize the principle, performance and application of the SMRT sequencing technology. Compared with the traditional Sanger method and the next-generation sequencing (NGS) technologies, the SMRT approach has several advantages, including long read length, high speed, PCR-free and the capability of direct detection of epigenetic modifications. However, the disadvantage of its low accuracy, most of which resulted from insertions and deletions, is also notable. So, the raw sequence data need to be corrected before assembly. Up to now, the SMRT is a good fit for applications in the de novo genomic sequencing and the high-quality assemblies of small genomes. In the future, it is expected to play an important role in epigenetics, transcriptomic sequencing, and assemblies of large genomes.

Evaluation of a real-time PCR assay based on the single-copy SAG1 gene for the detection of Toxoplasma gondii.

PubMed

Yu, Haijie; Huang, Bin; Zhuo, Xunhui; Chen, Xueqiu; Du, Aifang

2013-11-08

Real-time PCR-based detection of Toxoplasma gondii is very sensitive and convenient for diagnosing toxoplasmosis. However, the performance of the PCR assays could be influenced by the target gene chosen. Here we evaluate a real-time PCR assay using double-stranded DNA dyes (SYBR(®) Green I assay) with a new set of primers targeting the SAG1 gene for the fast and specific detection of T. gondii. The assay showed higher sensitivity than conventional PCR protocols using T. gondii DNA as template. The detection limit of the developed real-time PCR assay was in the order of 1 tachyzoite. The assay was also assessed by experimentally infected mice and showed positive results for blood (25%), spleen (50%) and lung (50%) as early as 1 dpi. The specificity of the assay was confirmed by using DNA from Neospora caninum, Escherichia coli, Babesia bovis, Trypanosoma brucei, Cryptosporidium parvum, and Toxocara canis. Assay applicability was successfully tested in blood samples collected from slaughtered pigs. These results indicate that, based on SYBR(®) green I, the quantitative SAG1 assay may also be useful in the study of the pathogenicity, immunoprophylaxis, and treatment of T. gondii. Copyright © 2013 Elsevier B.V. All rights reserved.

Development of a high-throughput detection system for HIV-1 using real-time NASBA based on molecular beacons

NASA Astrophysics Data System (ADS)

van Beuningen, Rinie; Marras, Salvatore A.; Kramer, Fred R.; Oosterlaken, Tom; Weusten, Jos; Borst, G.; van de Wiel, Paul

2001-04-01

HIV-1 viral load assays require accuracy and sensitivity at low RNA levels with the capability to detect all subtypes. Furthermore, the assay should be easy to perform and fast to be useful for routine diagnostics. In order to meet these demands we have combined isothermal NASBA amplification with molecular beacon probes for real-time detection and quantitation of HIV-1 RNA. Quantitation is based on co-amplification of the HIV-1 RNA in the clinical sample and a synthetic calibrator RNA which is amplified by the same primer set but detected with a differently labeled molecular beacon. The entire procedure is simple and analysis of 48 samples requires less than 1» hours with minimal hands-on time. A fluorescent plate reader is used for real-time detection and isothermal amplification. The linearity and precision of the assay was determined with the VQC HIV-1 type B standard of the Central Laboratory of the Dutch Red Cross Blood Banks, The Netherlands. Sensitivity was shown to be 50 copies per ml (cps/ml). The average assay precision was 0,19 log10 over a range of 100-300,000 cps/ml tested at nine concentrations. The linearity of dilution series of 15 cultured HIV-1 gag clades A-H was shown. The specificity was 100% on non HIV-1 samples HIV-2, HTLV-1 and HTLV-2. The assay robustness in terms of valid results was 99%. In conclusion, the new real-time NASBA assay meets state-of-the-art HIV-1 viral load performance requirements combined with a high level of user convenience.

Bacterial diversity and real-time PCR based assessment of linA and linB gene distribution at hexachlorocyclohexane contaminated sites.

PubMed

Lal, Devi; Jindal, Swati; Kumari, Hansi; Jit, Simran; Nigam, Aeshna; Sharma, Pooja; Kumari, Kirti; Lal, Rup

2015-03-01

The disposal of hexachlorocyclohexane (HCH) muck has created large number of HCH dumpsites all over the world from where the harmful HCH isomers are leaking into the environment. Bacteria have evolved at such contaminated sites that have the ability to degrade HCH. Degradation of various HCH isomers in bacterial strains is mediated primarily by two genes: linA and linB which encode dehydrochlorinase and haloalkane dehalogenase respectively. In this study we explored one such highly contaminated HCH dumpsite located in Lucknow, Uttar Pradesh, India. To assess the biostimulation potential of the contaminated site, microbial diversity study and real-time PCR based quantification of lin genes was carried out. The soil samples from dumpsite and surrounding areas were found to be highly contaminated with HCH residue levels as high as 1.8 × 10(5)  mg kg(-1). The residues were detected in areas upto 13 km from the dumpsite. Sphingomonads, Chromohalobacter, and Marinobacter were the dominant genera present at the dump-site. Role of Sphingomonads in HCH degradation has been well documented. The highest copy numbers of linA and linB genes as determined using real-time PCR were 6.2 × 10(4) and 5.3 × 10(5), respectively, were found in sample from the dump site. The presence of Sphingomonads, linA, and linB genes from HCH contaminated soil indicates the presence of indigenous bacterial communities capable of HCH degradation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of a real-time RT-PCR assay for a novel influenza A (H1N1) virus.

PubMed

Jiang, Tao; Kang, Xiaoping; Deng, Yongqiang; Zhao, Hui; Li, Xiaofeng; Yu, Xuedong; Yu, Man; Qin, Ede; Zhu, Qingyu; Yang, Yinhui; Qin, Chengfeng

2010-02-01

A pandemic caused by a novel influenza A virus (H1N1) poses a serious public health threat. In this study, a real-time reverse transcriptase PCR (RT-PCR) assay based on the hemagglutinin gene was developed that discriminates the novel H1N1 from swine influenza virus, seasonal H1N1/H3N2 virus and the highly pathogenic H5N1 avian influenza virus. The sensitivity of this assay was 0.2 50% tissue culture infective dose of virus and 200 copies of in vitro-transcribed target RNA. Three hundred and forty-eight clinical specimens from suspected H1N1 patients were tested using this assay, and forty-two (12.07%) were found to be positive. Tests using the real-time PCR assay recommended by WHO and virus isolation gave identical results. This sensitive and specific real-time RT-PCR assay will contribute to the early diagnosis and control of the emerging H1N1 influenza pandemic. 2009 Elsevier B.V. All rights reserved.

Culture and Real-Time PCR Based Maternal Screening and Antibiotic Susceptibility for Group B Streptococcus: An Iranian Experience.

PubMed

Goudarzi, Gholamreza; Ghafarzadeh, Masoumeh; Shakib, Pegah; Anbari, Khatereh

2015-04-19

Vertical Transmission of group B streptococcus (GBS) from a vagina colonized mother to her infant upon rupture of membranes (ROM) or after the onset of labor can cause life-threatening infections in newborn. Although intrapartum antibiotic prophylaxis (IAP) can significantly decrease neonatal GBS diseases, this issue has potentiated the emergence of antibiotic resistance strains. Our study examined the colonization rate of GBS using real-time PCR and culture methods, and trends in antibiotic resistance of GBS isolates obtained from pregnant women in Khorramabad, Iran. In this cross-sectional study, two vaginal-rectal swabs were collected and analyzed separately from 100 pregnant women at 35-37 weeks of gestation by convenience sampling method. The specimens were subjected to GBS detection using real-time PCR assay and standard culture. Susceptibility pattern of the GBS isolates was examined using the disk diffusion method. GBS carriage rate was 17% and 19% using culture and real-time PCR, respectively. In six samples, the culture was positive and the real-time PCR was negative. Sensitivity and specificity for real-time PCR were 72.7% and 96.1%, respectively using culture as the gold standard. Amongst twenty-two isolates examined, 100% resistance to erythromycin and clindamycin was observed. One isolate (4%) exhibited resistance to penicillin. Considering the relatively high GBS carriage rate in Khorramabad, routine antepartum screening for GBS is recommended. Penicillin can remain the antibiotic of choice for IAP; however, in penicillin-allergic mothers, vancomycin can be an alternative antibiotic.

Molecular Analysis of Spinal Muscular Atrophy: A genotyping protocol based on TaqMan(®) real-time PCR.

PubMed

de Souza Godinho, Fernanda Marques; Bock, Hugo; Gheno, Tailise Conte; Saraiva-Pereira, Maria Luiza

2012-12-01

Spinal muscular atrophy (SMA) is an autosomal recessive inherited disorder caused by alterations in the survival motor neuron I (SMN1) gene. SMA patients are classified as type I-IV based on severity of symptoms and age of onset. About 95% of SMA cases are caused by the homozygous absence of SMN1 due to gene deletion or conversion into SMN2. PCR-based methods have been widely used in genetic testing for SMA. In this work, we introduce a new approach based on TaqMan(®)real-time PCR for research and diagnostic settings. DNA samples from 100 individuals with clinical signs and symptoms suggestive of SMA were analyzed. Mutant DNA samples as well as controls were confirmed by DNA sequencing. We detected 58 SMA cases (58.0%) by showing deletion of SMN1 exon 7. Considering clinical information available from 56 of them, the patient distribution was 26 (46.4%) SMA type I, 16 (28.6%) SMA type II and 14 (25.0%) SMA type III. Results generated by the new method was confirmed by PCR-RFLP and by DNA sequencing when required. In conclusion, a protocol based on real-time PCR was shown to be effective and specific for molecular analysis of SMA patients.

Quantitative assessment of hematopoietic chimerism by quantitative real-time polymerase chain reaction of sequence polymorphism systems after hematopoietic stem cell transplantation.

PubMed

Qin, Xiao-ying; Li, Guo-xuan; Qin, Ya-zhen; Wang, Yu; Wang, Feng-rong; Liu, Dai-hong; Xu, Lan-ping; Chen, Huan; Han, Wei; Wang, Jing-zhi; Zhang, Xiao-hui; Li, Jin-lan; Li, Ling-di; Liu, Kai-yan; Huang, Xiao-jun

2011-08-01

Analysis of changes in recipient and donor hematopoietic cell origin is extremely useful to monitor the effect of hematopoietic stem cell transplantation (HSCT) and sequential adoptive immunotherapy by donor lymphocyte infusions. We developed a sensitive, reliable and rapid real-time PCR method based on sequence polymorphism systems to quantitatively assess the hematopoietic chimerism after HSCT. A panel of 29 selected sequence polymorphism (SP) markers was screened by real-time PCR in 101 HSCT patients with leukemia and other hematological diseases. The chimerism kinetics of bone marrow samples of 8 HSCT patients in remission and relapse situations were followed longitudinally. Recipient genotype discrimination was possible in 97.0% (98 of 101) with a mean number of 2.5 (1-7) informative markers per recipient/donor pair. Using serial dilutions of plasmids containing specific SP markers, the linear correlation (r) of 0.99, the slope between -3.2 and -3.7 and the sensitivity of 0.1% were proved reproducible. By this method, it was possible to very accurately detect autologous signals in the range from 0.1% to 30%. The accuracy of the method in the very important range of autologous signals below 5% was extraordinarily high (standard deviation <1.85%), which might significantly improve detection accuracy of changes in autologous signals early in the post-transplantation course of follow-up. The main advantage of the real-time PCR method over short tandem repeat PCR chimerism assays is the absence of PCR competition and plateau biases, with demonstrated greater sensitivity and linearity. Finally, we prospectively analyzed bone marrow samples of 8 patients who received allografts and presented the chimerism kinetics of remission and relapse situations that illustrated the sensitivity level and the promising clinical application of this method. This SP-based real-time PCR assay provides a rapid, sensitive, and accurate quantitative assessment of mixed chimerism that can

The L2b real-time PCR targeting the pmpH gene of Chlamydia trachomatis used for the diagnosis of lymphogranuloma venereum is not specific to L2b strains.

PubMed

Touati, A; Peuchant, O; Hénin, N; Bébéar, C; de Barbeyrac, B

2016-06-01

The French Reference Centre for chlamydiae uses two real-time PCRs targeting the pmpH gene of Chlamydia trachomatis to differentiate between L strains and variant L2b, responsible for a lymphogranuloma venereum outbreak in Europe. We compared the results obtained for 122 L2b C. trachomatis-positive specimens, using the two real-time PCRs, with the sequencing of the ompA gene. Only 91 specimens were confirmed as L2b. Our results demonstrate that the lymphogranuloma venereum outbreak is no longer dominated by the variant L2b, and that many L-positive specimens were misidentified as L2b with the method used, which raises the question of its specificity. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Evolution of simeprevir-resistant variants over time by ultra-deep sequencing in HCV genotype 1b.

PubMed

Akuta, Norio; Suzuki, Fumitaka; Sezaki, Hitomi; Suzuki, Yoshiyuki; Hosaka, Tetsuya; Kobayashi, Masahiro; Kobayashi, Mariko; Saitoh, Satoshi; Ikeda, Kenji; Kumada, Hiromitsu

2014-08-01

Using ultra-deep sequencing technology, the present study was designed to investigate the evolution of simeprevir-resistant variants (amino acid substitutions of aa80, aa155, aa156, and aa168 positions in HCV NS3 region) over time. In Toranomon Hospital, 18 Japanese patients infected with HCV genotype 1b, received triple therapy of simeprevir/PEG-IFN/ribavirin (DRAGON or CONCERT study). Sustained virological response rate was 67%, and that was significantly higher in patients with IL28B rs8099917 TT than in those with non-TT. Six patients, who did not achieve sustained virological response, were tested for resistant variants by ultra-deep sequencing, at the baseline, at the time of re-elevation of viral loads, and at 96 weeks after the completion of treatment. Twelve of 18 resistant variants, detected at re-elevation of viral load, were de novo resistant variants. Ten of 12 de novo resistant variants become undetectable over time, and that five of seven resistant variants, detected at baseline, persisted over time. In one patient, variants of Q80R at baseline (0.3%) increased at 96-week after the cessation of treatment (10.2%), and de novo resistant variants of D168E (0.3%) also increased at 96-week after the cessation of treatment (9.7%). In conclusion, the present study indicates that the emergence of simeprevir-resistant variants after the start of treatment could not be predicted at baseline, and the majority of de novo resistant variants become undetectable over time. Further large-scale prospective studies should be performed to investigate the clinical utility in detecting simeprevir-resistant variants. © 2014 Wiley Periodicals, Inc.

StarBase: A Firm Real-Time Database Manager for Time-Critical Applications

DTIC Science & Technology

1995-01-01

Mellon University [IO]. StarBase differs from previous RT-DBMS work [l, 2, 31 in that a) it relies on a real - time operating system which provides...simulation studies, StarBase uses a real - time operating system to provide basic real-time functionality and deals with issues beyond transaction...re- source scheduling provided by the underlying real - time operating system . Issues of data contention are dealt with by use of a priority

Cluster-Based Multipolling Sequencing Algorithm for Collecting RFID Data in Wireless LANs

NASA Astrophysics Data System (ADS)

Choi, Woo-Yong; Chatterjee, Mainak

2015-03-01

With the growing use of RFID (Radio Frequency Identification), it is becoming important to devise ways to read RFID tags in real time. Access points (APs) of IEEE 802.11-based wireless Local Area Networks (LANs) are being integrated with RFID networks that can efficiently collect real-time RFID data. Several schemes, such as multipolling methods based on the dynamic search algorithm and random sequencing, have been proposed. However, as the number of RFID readers associated with an AP increases, it becomes difficult for the dynamic search algorithm to derive the multipolling sequence in real time. Though multipolling methods can eliminate the polling overhead, we still need to enhance the performance of the multipolling methods based on random sequencing. To that extent, we propose a real-time cluster-based multipolling sequencing algorithm that drastically eliminates more than 90% of the polling overhead, particularly so when the dynamic search algorithm fails to derive the multipolling sequence in real time.

Draft Genome Sequence of Pseudomonas sp. Strain B1, Isolated from a Contaminated Sediment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pathak, Ashish; Jaswal, Rajneesh; Stothard, Paul

ABSTRACT The draft genome sequence of Pseudomonas sp. strain B1, isolated from a contaminated soil, is reported. The genome comprises 6,706,934 bases, 6,059 coding sequences, and 70 RNAs and has a G+C content of 60.3%. A suite of biodegradative genes, many located on genomic islands, were identified from strain B1, further enhancing our understanding of the versatile pseudomonads.

Draft Genome Sequence of Pseudomonas sp. Strain B1, Isolated from a Contaminated Sediment

DOE PAGES

Pathak, Ashish; Jaswal, Rajneesh; Stothard, Paul; ...

2018-06-21

ABSTRACT The draft genome sequence of Pseudomonas sp. strain B1, isolated from a contaminated soil, is reported. The genome comprises 6,706,934 bases, 6,059 coding sequences, and 70 RNAs and has a G+C content of 60.3%. A suite of biodegradative genes, many located on genomic islands, were identified from strain B1, further enhancing our understanding of the versatile pseudomonads.

Highly sensitive detection of mutations in CHO cell recombinant DNA using multi-parallel single molecule real-time DNA sequencing.

PubMed

Cartwright, Joseph F; Anderson, Karin; Longworth, Joseph; Lobb, Philip; James, David C

2018-06-01

High-fidelity replication of biologic-encoding recombinant DNA sequences by engineered mammalian cell cultures is an essential pre-requisite for the development of stable cell lines for the production of biotherapeutics. However, immortalized mammalian cells characteristically exhibit an increased point mutation frequency compared to mammalian cells in vivo, both across their genomes and at specific loci (hotspots). Thus unforeseen mutations in recombinant DNA sequences can arise and be maintained within producer cell populations. These may affect both the stability of recombinant gene expression and give rise to protein sequence variants with variable bioactivity and immunogenicity. Rigorous quantitative assessment of recombinant DNA integrity should therefore form part of the cell line development process and be an essential quality assurance metric for instances where synthetic/multi-component assemblies are utilized to engineer mammalian cells, such as the assessment of recombinant DNA fidelity or the mutability of single-site integration target loci. Based on Pacific Biosciences (Menlo Park, CA) single molecule real-time (SMRT™) circular consensus sequencing (CCS) technology we developed a rDNA sequence analysis tool to process the multi-parallel sequencing of ∼40,000 single recombinant DNA molecules. After statistical filtering of raw sequencing data, we show that this analytical method is capable of detecting single point mutations in rDNA to a minimum single mutation frequency of 0.0042% (<1/24,000 bases). Using a stable CHO transfectant pool harboring a randomly integrated 5 kB plasmid construct encoding GFP we found that 28% of recombinant plasmid copies contained at least one low frequency (<0.3%) point mutation. These mutations were predominantly found in GC base pairs (85%) and that there was no positional bias in mutation across the plasmid sequence. There was no discernable difference between the mutation frequencies of coding and non

Effect of Sequence Polymorphisms on Performance of Two Real-Time PCR Assays for Detection of Herpes Simplex Virus

PubMed Central

Stevenson, Jeffery; Hymas, Weston; Hillyard, David

2005-01-01

Herpes simplex virus (HSV) is the most common cause of acquired, sporadic encephalitis in the United States. PCR identification of HSV in spinal fluid has become the diagnostic gold standard due to its sensitivity and potential for speed, replacing other methods such as culture. We developed a real-time PCR assay to detect HSV, using a new type of hybridization probe, the Eclipse probe. In this study, we ran 323 samples (171 positives and 152 negatives) with the Eclipse real-time PCR assay and compared these results with another PCR assay using gel detection. The real-time assay agreed with our reference method for 319 out of the 323 samples tested (99%). Using two different real-time PCR platforms, we discovered that SNPs within the amplicon's probe binding region that are used to distinguish HSV-1 from HSV-2 can decrease assay sensitivity. This problem is potentially a general one for assays using fluorescent probes to detect target amplification in a real-time format. While real-time PCR can be a powerful tool in the field of infectious disease, careful sequence evaluation and clinical validation are essential in creating an effective assay. PMID:15872272

MISR Level 1 Near Real Time Products

Atmospheric Science Data Center

2016-10-31

Level 1 Near Real Time The MISR Near Real Time Level 1 data products ... km MISR swath and projected onto a Space-Oblique Mercator (SOM) map grid. The Ellipsoid-projected and Terrain-projected top-of-atmosphere (TOA) radiance products provide measurements respectively resampled onto the ...

Real time animation of space plasma phenomena

NASA Technical Reports Server (NTRS)

Jordan, K. F.; Greenstadt, E. W.

1987-01-01

In pursuit of real time animation of computer simulated space plasma phenomena, the code was rewritten for the Massively Parallel Processor (MPP). The program creates a dynamic representation of the global bowshock which is based on actual spacecraft data and designed for three dimensional graphic output. This output consists of time slice sequences which make up the frames of the animation. With the MPP, 16384, 512 or 4 frames can be calculated simultaneously depending upon which characteristic is being computed. The run time was greatly reduced which promotes the rapid sequence of images and makes real time animation a foreseeable goal. The addition of more complex phenomenology in the constructed computer images is now possible and work proceeds to generate these images.

Time-stretch microscopy based on time-wavelength sequence reconstruction from wideband incoherent source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Chi, E-mail: chizheung@gmail.com; Xu, Yiqing; Wei, Xiaoming

2014-07-28

Time-stretch microscopy has emerged as an ultrafast optical imaging concept offering the unprecedented combination of the imaging speed and sensitivity. However, dedicated wideband and coherence optical pulse source with high shot-to-shot stability has been mandated for time-wavelength mapping—the enabling process for ultrahigh speed wavelength-encoded image retrieval. From the practical point of view, exploiting methods to relax the stringent requirements (e.g., temporal stability and coherence) for the source of time-stretch microscopy is thus of great value. In this paper, we demonstrated time-stretch microscopy by reconstructing the time-wavelength mapping sequence from a wideband incoherent source. Utilizing the time-lens focusing mechanism mediated bymore » a narrow-band pulse source, this approach allows generation of a wideband incoherent source, with the spectral efficiency enhanced by a factor of 18. As a proof-of-principle demonstration, time-stretch imaging with the scan rate as high as MHz and diffraction-limited resolution is achieved based on the wideband incoherent source. We note that the concept of time-wavelength sequence reconstruction from wideband incoherent source can also be generalized to any high-speed optical real-time measurements, where wavelength is acted as the information carrier.« less

A TaqMan-based real time PCR assay for specific detection and quantification of Xylella fastidiosa strains causing bacterial leaf scorch in oleander.

PubMed

Guan, Wei; Shao, Jonathan; Singh, Raghuwinder; Davis, Robert E; Zhao, Tingchang; Huang, Qi

2013-02-15

A TaqMan-based real-time PCR assay was developed for specific detection of strains of X. fastidiosa causing oleander leaf scorch. The assay uses primers WG-OLS-F1 and WG-OLS-R1 and the fluorescent probe WG-OLS-P1, designed based on unique sequences found only in the genome of oleander strain Ann1. The assay is specific, allowing detection of only oleander-infecting strains, not other strains of X. fastidiosa nor other plant-associated bacteria tested. The assay is also sensitive, with a detection limit of 10.4fg DNA of X. fastidiosa per reaction in vitro and in planta. The assay can also be applied to detect low numbers of X. fastidiosa in insect samples, or further developed into a multiplex real-time PCR assay to simultaneously detect and distinguish diverse strains of X. fastidiosa that may occupy the same hosts or insect vectors. Specific and sensitive detection and quantification of oleander strains of X. fastidiosa should be useful for disease diagnosis, epidemiological studies, management of oleander leaf scorch disease, and resistance screening for oleander shrubs. Published by Elsevier B.V.

Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA

PubMed Central

Jahan, Munira; Lutful Moben, Ahmed; Tabassum, Shahina

2014-01-01

ABSTRACT Background Both real-time-polymerase chain reaction (PCR) and hybrid capture 2 (HC2) assay can detect and quantify hepatitis B virus (HBV) DNA. However, real-time-PCR can detect a wide range of HBV DNA, while HC2 assay could not detect lower levels of viremia. The present study was designed to detect and quantify HBV DNA by real-time-PCR and HC2 assay and compare the quantitative data of these two assays. Materials and methods A cross-sectional study was conducted in between July 2010 and June 2011. A total of 66 serologically diagnosed chronic hepatitis B (CHB) patients were selected for the study. Real-time-PCR and HC2 assay was done to detect HBV DNA. Data were analyzed by statistical Package for the social sciences (SPSS). Results Among 66 serologically diagnosed chronic hepatitis B patients 40 (60.61%) patients had detectable and 26 (39.39%) had undetectable HBV DNA by HC2 assay. Concordant results were obtained for 40 (60.61%) out of these 66 patients by real-time-PCR and HC2 assay with mean viral load of 7.06 ± 1.13 log10 copies/ml and 6.95 ± 1.08 log10 copies/ml, respectively. In the remaining 26 patients, HBV DNA was detectable by real-time-PCR in 20 patients (mean HBV DNA level was 3.67 ± 0.72 log10 copies/ml. However, HBV DNA could not be detectable in six cases by the both assays. The study showed strong correlation (r = 0.915) between real-time-PCR and HC2 assay for the detection and quantification of HBV DNA. Conclusion HC2 assay may be used as an alternative to real-time-PCR for CHB patients. How to cite this article: Majid F, Jahan M, Moben AL, Tabassum S. Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA. Euroasian J Hepato-Gastroenterol 2014;4(1):31-35. PMID:29264316

Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA.

PubMed

Majid, Farjana; Jahan, Munira; Lutful Moben, Ahmed; Tabassum, Shahina

2014-01-01

Both real-time-polymerase chain reaction (PCR) and hybrid capture 2 (HC2) assay can detect and quantify hepatitis B virus (HBV) DNA. However, real-time-PCR can detect a wide range of HBV DNA, while HC2 assay could not detect lower levels of viremia. The present study was designed to detect and quantify HBV DNA by real-time-PCR and HC2 assay and compare the quantitative data of these two assays. A cross-sectional study was conducted in between July 2010 and June 2011. A total of 66 serologically diagnosed chronic hepatitis B (CHB) patients were selected for the study. Real-time-PCR and HC2 assay was done to detect HBV DNA. Data were analyzed by statistical Package for the social sciences (SPSS). Among 66 serologically diagnosed chronic hepatitis B patients 40 (60.61%) patients had detectable and 26 (39.39%) had undetectable HBV DNA by HC2 assay. Concordant results were obtained for 40 (60.61%) out of these 66 patients by real-time-PCR and HC2 assay with mean viral load of 7.06 ± 1.13 log 10 copies/ml and 6.95 ± 1.08 log 10 copies/ml, respectively. In the remaining 26 patients, HBV DNA was detectable by real-time-PCR in 20 patients (mean HBV DNA level was 3.67 ± 0.72 log 10 copies/ml. However, HBV DNA could not be detectable in six cases by the both assays. The study showed strong correlation (r = 0.915) between real-time-PCR and HC2 assay for the detection and quantification of HBV DNA. HC2 assay may be used as an alternative to real-time-PCR for CHB patients. How to cite this article: Majid F, Jahan M, Moben AL, Tabassum S. Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA. Euroasian J Hepato-Gastroenterol 2014;4(1):31-35.

Development of internally controlled duplex real-time NASBA diagnostics assays for the detection of microorganisms associated with bacterial meningitis.

PubMed

Clancy, Eoin; Coughlan, Helena; Higgins, Owen; Boo, Teck Wee; Cormican, Martin; Barrett, Louise; Smith, Terry J; Reddington, Kate; Barry, Thomas

2016-08-01

Three duplex molecular beacon based real-time Nucleic Acid Sequence Based Amplification (NASBA) assays have been designed and experimentally validated targeting RNA transcripts for the detection and identification of Haemophilus influenzae, Neisseria meningitidis and Streptococcus pneumoniae respectively. Each real-time NASBA diagnostics assay includes an endogenous non-competitive Internal Amplification Control (IAC) to amplify the splice variant 1 mRNA of the Homo sapiens TBP gene from human total RNA. All three duplex real-time NASBA diagnostics assays were determined to be 100% specific for the target species tested for. Also the Limits of Detection (LODs) for the H. influenzae, N. meningitidis and S. pneumoniae duplex real-time NASBA assays were 55.36, 0.99, and 57.24 Cell Equivalents (CE) respectively. These robust duplex real-time NASBA diagnostics assays have the potential to be used in a clinical setting for the rapid (<60min) specific detection and identification of the most prominent microorganisms associated with bacterial meningitis in humans. Copyright © 2016 Elsevier B.V. All rights reserved.

SNP-based real-time pyrosequencing as a sensitive and specific tool for identification and differentiation of Rickettsia species in Ixodes ricinus ticks.

PubMed

Janecek, Elisabeth; Streichan, Sabine; Strube, Christina

2012-10-18

Rickettsioses are caused by pathogenic species of the genus Rickettsia and play an important role as emerging diseases. The bacteria are transmitted to mammal hosts including humans by arthropod vectors. Since detection, especially in tick vectors, is usually based on PCR with genus-specific primers to include different occurring Rickettsia species, subsequent species identification is mainly achieved by Sanger sequencing. In the present study a real-time pyrosequencing approach was established with the objective to differentiate between species occurring in German Ixodes ticks, which are R. helvetica, R. monacensis, R. massiliae, and R. felis. Tick material from a quantitative real-time PCR (qPCR) based study on Rickettsia-infections in I. ricinus allowed direct comparison of both sequencing techniques, Sanger and real-time pyrosequencing. A sequence stretch of rickettsial citrate synthase (gltA) gene was identified to contain divergent single nucleotide polymorphism (SNP) sites suitable for Rickettsia species differentiation. Positive control plasmids inserting the respective target sequence of each Rickettsia species of interest were constructed for initial establishment of the real-time pyrosequencing approach using Qiagen's PSQ 96MA Pyrosequencing System operating in a 96-well format. The approach included an initial amplification reaction followed by the actual pyrosequencing, which is traceable by pyrograms in real-time. Afterwards, real-time pyrosequencing was applied to 263 Ixodes tick samples already detected Rickettsia-positive in previous qPCR experiments. Establishment of real-time pyrosequencing using positive control plasmids resulted in accurate detection of all SNPs in all included Rickettsia species. The method was then applied to 263 Rickettsia-positive Ixodes ricinus samples, of which 153 (58.2%) could be identified for their species (151 R. helvetica and 2 R. monacensis) by previous custom Sanger sequencing. Real-time pyrosequencing identified

Complete genome sequence of Pelosinus sp. strain UFO1 assembled using single-molecule real-time DNA sequencing technology

DOE PAGES

Brown, Steven D.; Utturkar, Sagar M.; Magnuson, Timothy S.; ...

2014-09-04

Pelosinus fermentans strain R7 was isolated from Russian kaolin clays as the type strain and it can reduce Fe(III) during fermentative growth (1). Draft genome sequences for P. fermentans R7 and four strains from Hanford, Washington, USA, have been published (2–4). The P. fermentans 16S rRNA sequence dominated the lactate-based enrichment cultures from three geochemically contrasting soils from the Melton Branch Watershed, Oak Ridge, Tennessee, USA (5) and also at another stimulated, uraniumcontaminated field site near Oak Ridge (6). For the current work, strain UFO1 was isolated from pristine sediments at a background field site in Oak Ridge and characterizedmore » as facilitating U(VI) reduction and precipitation with phosphate (7).« less

A TaqMan real-time PCR-based assay for the identification of Fasciola spp.

PubMed

Alasaad, Samer; Soriguer, Ramón C; Abu-Madi, Marawan; El Behairy, Ahmed; Jowers, Michael J; Baños, Pablo Díez; Píriz, Ana; Fickel, Joerns; Zhu, Xing-Quan

2011-06-30

Real time quantitative PCR (qPCR) is one of the key technologies of the post-genome era, with clear advantages compared to normal end-point PCR. In this paper, we report the first qPCR-based assay for the identification of Fasciola spp. Based on sequences of the second internal transcribed spacers (ITS-2) of the ribosomal rRNA gene, we used a set of genus-specific primers for Fasciola ITS-2 amplification, and we designed species-specific internal TaqMan probes to identify F. hepatica and F. gigantica, as well as the hybrid 'intermediate'Fasciola. These primers and probes were used for the highly specific, sensitive, and simple identification of Fasciola species collected from different animal host from China, Spain, Niger and Egypt. The novel qPCR-based technique for the identification of Fasciola spp. may provide a useful tool for the epidemiological investigation of Fasciola infection, including their intermediate snail hosts. Copyright © 2011 Elsevier B.V. All rights reserved.

DNA barcoding and real-time PCR detection of Bactrocera xanthodes (Tephritidae: Diptera) complex.

PubMed

Li, D; Waite, D W; Gunawardana, D N; McCarthy, B; Anderson, D; Flynn, A; George, S

2018-05-06

Immature fruit fly stages of the family Tephritidae are commonly intercepted on breadfruit from Pacific countries at the New Zealand border but are unable to be identified to the species level using morphological characters. Subsequent molecular identification showed that they belong to Bactrocera xanthodes, which is part of a species complex that includes Bactrocera paraxanthodes, Bactrocera neoxanthodes and an undescribed species. To establish a more reliable molecular identification system for B. xanthodes, a reference database of DNA barcode sequences for the 5'-fragment of COI gene region was constructed for B. xanthodes from Fiji, Samoa and Tonga. To better understand the species complex, B. neoxanthodes from Vanuatu and B. paraxanthodes from New Caledonia were also barcoded. Using the results of this analysis, real-time TaqMan polymerase chain reaction (PCR) assays for the detection of B. xanthodes complex and for the three individual species of the complex were developed and validated. The assay showed high specificity for the target species, with no cross-reaction observed for closely related organisms. Each of the real-time PCR assays is sensitive, detecting the target sequences at concentrations as low as ten copies µl-1 and can be used as either singleplex or multiplex formats. This real-time PCR assay for B. xanthodes has been successfully applied at the borders in New Zealand, leading to the rapid identification of intercepted Tephritidae eggs and larvae. The developed assays will be useful biosecurity tools for rapid detection of species in the B. xanthodes complex worldwide.

Real-time fast physical random number generator with a photonic integrated circuit.

PubMed

Ugajin, Kazusa; Terashima, Yuta; Iwakawa, Kento; Uchida, Atsushi; Harayama, Takahisa; Yoshimura, Kazuyuki; Inubushi, Masanobu

2017-03-20

Random number generators are essential for applications in information security and numerical simulations. Most optical-chaos-based random number generators produce random bit sequences by offline post-processing with large optical components. We demonstrate a real-time hardware implementation of a fast physical random number generator with a photonic integrated circuit and a field programmable gate array (FPGA) electronic board. We generate 1-Tbit random bit sequences and evaluate their statistical randomness using NIST Special Publication 800-22 and TestU01. All of the BigCrush tests in TestU01 are passed using 410-Gbit random bit sequences. A maximum real-time generation rate of 21.1 Gb/s is achieved for random bit sequences in binary format stored in a computer, which can be directly used for applications involving secret keys in cryptography and random seeds in large-scale numerical simulations.

Real-time polymerase chain reaction assay for rapid and sensitive detection of anthrax spores in spiked soil and talcum powder.

PubMed

Jain, Neha; Merwyn, S; Rai, G P; Agarwal, G S

2012-05-01

Real-time polymerase chain reaction (real-time PCR) is a laboratory technique based on PCR. This technique is able to detect sequence-specific PCR products as they accumulate in "real time" during the PCR amplification, and also to quantify the number of substrates present in the initial PCR mixture before amplification begins. In the present study, real-time PCR assay was employed for rapid and real-time detection of Bacillus anthracis spores spiked in 0.1 g of soil and talcum powder ranging from 5 to 10(7) spores. DNA was isolated from spiked soil and talcum powder, using PBS containing 1 % Triton-X-100, followed by heat treatment. The isolated DNA was used as template for real-time PCR and PCR. Real-time PCR amplification was obtained in 60 min under the annealing condition at 60°C by employing primers targeting the pag gene of B. anthracis. In the present study, the detection limit of real-time PCR assay in soil was 10(3) spores and 10(2) spores in talcum powder, respectively, whereas PCR could detect 10(4) spores in soil and 10(3) spores in talcum powder, respectively.

Performance Evaluation of a Firm Real-Time DataBase System

DTIC Science & Technology

1995-01-01

after its deadline has passed. StarBase differs from previous real-time database work in that a) it relies on a real - time operating system which...StarBase, running on a real - time operating system kernel, RT-Mach. We discuss how performance was evaluated in StarBase using the StarBase workload

FPGA-based architecture for real-time data reduction of ultrasound signals.

PubMed

Soto-Cajiga, J A; Pedraza-Ortega, J C; Rubio-Gonzalez, C; Bandala-Sanchez, M; Romero-Troncoso, R de J

2012-02-01

This paper describes a novel method for on-line real-time data reduction of radiofrequency (RF) ultrasound signals. The approach is based on a field programmable gate array (FPGA) system intended mainly for steel thickness measurements. Ultrasound data reduction is desirable when: (1) direct measurements performed by an operator are not accessible; (2) it is required to store a considerable amount of data; (3) the application requires measuring at very high speeds; and (4) the physical space for the embedded hardware is limited. All the aforementioned scenarios can be present in applications such as pipeline inspection where data reduction is traditionally performed on-line using pipeline inspection gauges (PIG). The method proposed in this work consists of identifying and storing in real-time only the time of occurrence (TOO) and the maximum amplitude of each echo present in a given RF ultrasound signal. The method is tested with a dedicated immersion system where a significant data reduction with an average of 96.5% is achieved. Copyright © 2011 Elsevier B.V. All rights reserved.

Detection and identification of genetically modified EE-1 brinjal (Solanum melongena) by single, multiplex and SYBR® real-time PCR.

PubMed

Ballari, Rajashekhar V; Martin, Asha; Gowda, Lalitha R

2013-01-01

Brinjal is an important vegetable crop. Major crop loss of brinjal is due to insect attack. Insect-resistant EE-1 brinjal has been developed and is awaiting approval for commercial release. Consumer health concerns and implementation of international labelling legislation demand reliable analytical detection methods for genetically modified (GM) varieties. End-point and real-time polymerase chain reaction (PCR) methods were used to detect EE-1 brinjal. In end-point PCR, primer pairs specific to 35S CaMV promoter, NOS terminator and nptII gene common to other GM crops were used. Based on the revealed 3' transgene integration sequence, primers specific for the event EE-1 brinjal were designed. These primers were used for end-point single, multiplex and SYBR-based real-time PCR. End-point single PCR showed that the designed primers were highly specific to event EE-1 with a sensitivity of 20 pg of genomic DNA, corresponding to 20 copies of haploid EE-1 brinjal genomic DNA. The limits of detection and quantification for SYBR-based real-time PCR assay were 10 and 100 copies respectively. The prior development of detection methods for this important vegetable crop will facilitate compliance with any forthcoming labelling regulations. Copyright © 2012 Society of Chemical Industry.

Simple Real-Time PCR and Amplicon Sequencing Method for Identification of Plasmodium Species in Human Whole Blood.

PubMed

Lefterova, Martina I; Budvytiene, Indre; Sandlund, Johanna; Färnert, Anna; Banaei, Niaz

2015-07-01

Malaria is the leading identifiable cause of fever in returning travelers. Accurate Plasmodium species identification has therapy implications for P. vivax and P. ovale, which have dormant liver stages requiring primaquine. Compared to microscopy, nucleic acid tests have improved specificity for species identification and higher sensitivity for mixed infections. Here, we describe a SYBR green-based real-time PCR assay for Plasmodium species identification from whole blood, which uses a panel of reactions to detect species-specific non-18S rRNA gene targets. A pan-Plasmodium 18S rRNA target is also amplified to allow species identification or confirmation by sequencing if necessary. An evaluation of assay accuracy, performed on 76 clinical samples (56 positives using thin smear microscopy as the reference method and 20 negatives), demonstrated clinical sensitivities of 95.2% for P. falciparum (20/21 positives detected) and 100% for the Plasmodium genus (52/52), P. vivax (20/20), P. ovale (9/9), and P. malariae (6/6). The sensitivity of the P. knowlesi-specific PCR was evaluated using spiked whole blood samples (100% [10/10 detected]). The specificities of the real-time PCR primers were 94.2% for P. vivax (49/52) and 100% for P. falciparum (51/51), P. ovale (62/62), P. malariae (69/69), and P. knowlesi (52/52). Thirty-three specimens were used to test species identification by sequencing the pan-Plasmodium 18S rRNA PCR product, with correct identification in all cases. The real-time PCR assay also identified two samples with mixed P. falciparum and P. ovale infection, which was confirmed by sequencing. The assay described here can be integrated into a malaria testing algorithm in low-prevalence areas, allowing definitive Plasmodium species identification shortly after malaria diagnosis by microscopy. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing.

PubMed

Nong, Rachel Yuan; Wu, Di; Yan, Junhong; Hammond, Maria; Gu, Gucci Jijuan; Kamali-Moghaddam, Masood; Landegren, Ulf; Darmanis, Spyros

2013-06-01

Solid-phase proximity ligation assays share properties with the classical sandwich immunoassays for protein detection. The proteins captured via antibodies on solid supports are, however, detected not by single antibodies with detectable functions, but by pairs of antibodies with attached DNA strands. Upon recognition by these sets of three antibodies, pairs of DNA strands brought in proximity are joined by ligation. The ligated reporter DNA strands are then detected via methods such as real-time PCR or next-generation sequencing (NGS). We describe how to construct assays that can offer improved detection specificity by virtue of recognition by three antibodies, as well as enhanced sensitivity owing to reduced background and amplified detection. Finally, we also illustrate how the assays can be applied for parallel detection of proteins, taking advantage of the oligonucleotide ligation step to avoid background problems that might arise with multiplexing. The protocol for the singleplex solid-phase proximity ligation assay takes ~5 h. The multiplex version of the assay takes 7-8 h depending on whether quantitative PCR (qPCR) or sequencing is used as the readout. The time for the sequencing-based protocol includes the library preparation but not the actual sequencing, as times may vary based on the choice of sequencing platform.

Real-time biscuit tile image segmentation method based on edge detection.

PubMed

Matić, Tomislav; Aleksi, Ivan; Hocenski, Željko; Kraus, Dieter

2018-05-01

In this paper we propose a novel real-time Biscuit Tile Segmentation (BTS) method for images from ceramic tile production line. BTS method is based on signal change detection and contour tracing with a main goal of separating tile pixels from background in images captured on the production line. Usually, human operators are visually inspecting and classifying produced ceramic tiles. Computer vision and image processing techniques can automate visual inspection process if they fulfill real-time requirements. Important step in this process is a real-time tile pixels segmentation. BTS method is implemented for parallel execution on a GPU device to satisfy the real-time constraints of tile production line. BTS method outperforms 2D threshold-based methods, 1D edge detection methods and contour-based methods. Proposed BTS method is in use in the biscuit tile production line. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing.

PubMed

Euskirchen, Philipp; Bielle, Franck; Labreche, Karim; Kloosterman, Wigard P; Rosenberg, Shai; Daniau, Mailys; Schmitt, Charlotte; Masliah-Planchon, Julien; Bourdeaut, Franck; Dehais, Caroline; Marie, Yannick; Delattre, Jean-Yves; Idbaih, Ahmed

2017-11-01

Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making. Here, we explored the potential of a pocket-size nanopore sequencing device for multimodal and rapid molecular diagnostics of cancer. Low-pass whole genome sequencing was used to simultaneously generate copy number (CN) and methylation profiles from native tumor DNA in the same sequencing run. Single nucleotide variants in IDH1, IDH2, TP53, H3F3A, and the TERT promoter region were identified using deep amplicon sequencing. Nanopore sequencing yielded ~0.1X genome coverage within 6 h and resulting CN and epigenetic profiles correlated well with matched microarray data. Diagnostically relevant alterations, such as 1p/19q codeletion, and focal amplifications could be recapitulated. Using ad hoc random forests, we could perform supervised pan-cancer classification to distinguish gliomas, medulloblastomas, and brain metastases of different primary sites. Single nucleotide variants in IDH1, IDH2, and H3F3A were identified using deep amplicon sequencing within minutes of sequencing. Detection of TP53 and TERT promoter mutations shows that sequencing of entire genes and GC-rich regions is feasible. Nanopore sequencing allows same-day detection of structural variants, point mutations, and methylation profiling using a single device with negligible capital cost. It

Real-time tracking of respiratory-induced tumor motion by dose-rate regulation

NASA Astrophysics Data System (ADS)

Han-Oh, Yeonju Sarah

We have developed a novel real-time tumor-tracking technology, called Dose-Rate-Regulated Tracking (DRRT), to compensate for tumor motion caused by breathing. Unlike other previously proposed tumor-tracking methods, this new method uses a preprogrammed dynamic multileaf collimator (MLC) sequence in combination with real-time dose-rate control. This new scheme circumvents the technical challenge in MLC-based tumor tracking, that is to control the MLC motion in real time, based on real-time detected tumor motion. The preprogrammed MLC sequence describes the movement of the tumor, as a function of breathing phase, amplitude, or tidal volume. The irregularity of tumor motion during treatment is handled by real-time regulation of the dose rate, which effectively speeds up or slows down the delivery of radiation as needed. This method is based on the fact that all of the parameters in dynamic radiation delivery, including MLC motion, are enslaved to the cumulative dose, which, in turn, can be accelerated or decelerated by varying the dose rate. Because commercially available MLC systems do not allow the MLC delivery sequence to be modified in real time based on the patient's breathing signal, previously proposed tumor-tracking techniques using a MLC cannot be readily implemented in the clinic today. By using a preprogrammed MLC sequence to handle the required motion, the task for real-time control is greatly simplified. We have developed and tested the pre- programmed MLC sequence and the dose-rate regulation algorithm using lung-cancer patients breathing signals. It has been shown that DRRT can track the tumor with an accuracy of less than 2 mm for a latency of the DRRT system of less than 0.35 s. We also have evaluated the usefulness of guided breathing for DRRT. Since DRRT by its very nature can compensate for breathing-period changes, guided breathing was shown to be unnecessary for real-time tracking when using DRRT. Finally, DRRT uses the existing dose-rate control

A real-time spike sorting method based on the embedded GPU.

PubMed

Zelan Yang; Kedi Xu; Xiang Tian; Shaomin Zhang; Xiaoxiang Zheng

2017-07-01

Microelectrode arrays with hundreds of channels have been widely used to acquire neuron population signals in neuroscience studies. Online spike sorting is becoming one of the most important challenges for high-throughput neural signal acquisition systems. Graphic processing unit (GPU) with high parallel computing capability might provide an alternative solution for increasing real-time computational demands on spike sorting. This study reported a method of real-time spike sorting through computing unified device architecture (CUDA) which was implemented on an embedded GPU (NVIDIA JETSON Tegra K1, TK1). The sorting approach is based on the principal component analysis (PCA) and K-means. By analyzing the parallelism of each process, the method was further optimized in the thread memory model of GPU. Our results showed that the GPU-based classifier on TK1 is 37.92 times faster than the MATLAB-based classifier on PC while their accuracies were the same with each other. The high-performance computing features of embedded GPU demonstrated in our studies suggested that the embedded GPU provide a promising platform for the real-time neural signal processing.

A Real-Time Executive for Multiple-Computer Clusters.

DTIC Science & Technology

1984-12-01

in a real-time environment is tantamount to speed and efficiency. By effectively co-locating real-time sensors and related processing modules, real...of which there are two ki n1 s : multicast group address - virtually any nur.,ber of node groups can be assigned a group address so they are all able...interfaceloopbark by 󈧅’b4, internal _loopback by 02"b4, clear loooback by 󈧇’b4, go offline by Ŝ"b4, eo online by 󈧍’b4, onboard _diagnostic by Oa’b4, cdr

FPGA-based architecture for motion recovering in real-time

NASA Astrophysics Data System (ADS)

Arias-Estrada, Miguel; Maya-Rueda, Selene E.; Torres-Huitzil, Cesar

2002-03-01

A key problem in the computer vision field is the measurement of object motion in a scene. The main goal is to compute an approximation of the 3D motion from the analysis of an image sequence. Once computed, this information can be used as a basis to reach higher level goals in different applications. Motion estimation algorithms pose a significant computational load for the sequential processors limiting its use in practical applications. In this work we propose a hardware architecture for motion estimation in real time based on FPGA technology. The technique used for motion estimation is Optical Flow due to its accuracy, and the density of velocity estimation, however other techniques are being explored. The architecture is composed of parallel modules working in a pipeline scheme to reach high throughput rates near gigaflops. The modules are organized in a regular structure to provide a high degree of flexibility to cover different applications. Some results will be presented and the real-time performance will be discussed and analyzed. The architecture is prototyped in an FPGA board with a Virtex device interfaced to a digital imager.

Comparative Genomic Analysis of Two Clonally Related Multidrug Resistant Mycobacterium tuberculosis by Single Molecule Real Time Sequencing.

PubMed

Leung, Kenneth Siu-Sing; Siu, Gilman Kit-Hang; Tam, Kingsley King-Gee; To, Sabrina Wai-Chi; Rajwani, Rahim; Ho, Pak-Leung; Wong, Samson Sai-Yin; Zhao, Wei W; Ma, Oliver Chiu-Kit; Yam, Wing-Cheong

2017-01-01

Background: Multidrug-resistant tuberculosis (MDR-TB) is posing a major threat to global TB control. In this study, we focused on two consecutive MDR-TB isolated from the same patient before and after the initiation of anti-TB treatment. To better understand the genomic characteristics of MDR-TB, Single Molecule Real-Time (SMRT) Sequencing and comparative genomic analyses was performed to identify mutations that contributed to the stepwise development of drug resistance and growth fitness in MDR-TB under in vivo challenge of anti-TB drugs. Result: Both pre-treatment and post-treatment strain demonstrated concordant phenotypic and genotypic susceptibility profiles toward rifampicin, pyrazinamide, streptomycin, fluoroquinolones, aminoglycosides, cycloserine, ethionamide, and para-aminosalicylic acid. However, although both strains carried identical missense mutations at rpoB S531L, inhA C-15T, and embB M306V, MYCOTB Sensititre assay showed that the post-treatment strain had 16-, 8-, and 4-fold elevation in the minimum inhibitory concentrations (MICs) toward rifabutin, isoniazid, and ethambutol respectively. The results have indicated the presence of additional resistant-related mutations governing the stepwise development of MDR-TB. Further comparative genomic analyses have identified three additional polymorphisms between the clinical isolates. These include a single nucleotide deletion at nucleotide position 360 of rv0888 in pre-treatment strain, and a missense mutation at rv3303c ( lpdA) V44I and a 6-bp inframe deletion at codon 67-68 in rv2071c ( cobM) in the post-treatment strain. Multiple sequence alignment showed that these mutations were occurring at highly conserved regions among pathogenic mycobacteria. Using structural-based and sequence-based algorithms, we further predicted that the mutations potentially have deleterious effect on protein function. Conclusion: This is the first study that compared the full genomes of two clonally-related MDR-TB clinical

PRAIS: Distributed, real-time knowledge-based systems made easy

NASA Technical Reports Server (NTRS)

Goldstein, David G.

1990-01-01

This paper discusses an architecture for real-time, distributed (parallel) knowledge-based systems called the Parallel Real-time Artificial Intelligence System (PRAIS). PRAIS strives for transparently parallelizing production (rule-based) systems, even when under real-time constraints. PRAIS accomplishes these goals by incorporating a dynamic task scheduler, operating system extensions for fact handling, and message-passing among multiple copies of CLIPS executing on a virtual blackboard. This distributed knowledge-based system tool uses the portability of CLIPS and common message-passing protocols to operate over a heterogeneous network of processors.

Real time magnetic resonance guided endomyocardial local delivery

PubMed Central

Corti, R; Badimon, J; Mizsei, G; Macaluso, F; Lee, M; Licato, P; Viles-Gonzalez, J F; Fuster, V; Sherman, W

2005-01-01

Objective: To investigate the feasibility of targeting various areas of left ventricle myocardium under real time magnetic resonance (MR) imaging with a customised injection catheter equipped with a miniaturised coil. Design: A needle injection catheter with a mounted resonant solenoid circuit (coil) at its tip was designed and constructed. A 1.5 T MR scanner with customised real time sequence combined with in-room scan running capabilities was used. With this system, various myocardial areas within the left ventricle were targeted and injected with a gadolinium-diethylenetriaminepentaacetic acid (DTPA) and Indian ink mixture. Results: Real time sequencing at 10 frames/s allowed clear visualisation of the moving catheter and its transit through the aorta into the ventricle, as well as targeting of all ventricle wall segments without further image enhancement techniques. All injections were visualised by real time MR imaging and verified by gross pathology. Conclusion: The tracking device allowed real time in vivo visualisation of catheters in the aorta and left ventricle as well as precise targeting of myocardial areas. The use of this real time catheter tracking may enable precise and adequate delivery of agents for tissue regeneration. PMID:15710717

A Lyapunov Function Based Remedial Action Screening Tool Using Real-Time Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mitra, Joydeep; Ben-Idris, Mohammed; Faruque, Omar

This report summarizes the outcome of a research project that comprised the development of a Lyapunov function based remedial action screening tool using real-time data (L-RAS). The L-RAS is an advanced computational tool that is intended to assist system operators in making real-time redispatch decisions to preserve power grid stability. The tool relies on screening contingencies using a homotopy method based on Lyapunov functions to avoid, to the extent possible, the use of time domain simulations. This enables transient stability evaluation at real-time speed without the use of massively parallel computational resources. The project combined the following components. 1. Developmentmore » of a methodology for contingency screening using a homotopy method based on Lyapunov functions and real-time data. 2. Development of a methodology for recommending remedial actions based on the screening results. 3. Development of a visualization and operator interaction interface. 4. Testing of screening tool, validation of control actions, and demonstration of project outcomes on a representative real system simulated on a Real-Time Digital Simulator (RTDS) cluster. The project was led by Michigan State University (MSU), where the theoretical models including homotopy-based screening, trajectory correction using real-time data, and remedial action were developed and implemented in the form of research-grade software. Los Alamos National Laboratory (LANL) contributed to the development of energy margin sensitivity dynamics, which constituted a part of the remedial action portfolio. Florida State University (FSU) and Southern California Edison (SCE) developed a model of the SCE system that was implemented on FSU's RTDS cluster to simulate real-time data that was streamed over the internet to MSU where the L-RAS tool was executed and remedial actions were communicated back to FSU to execute stabilizing controls on the simulated system. LCG Consulting developed the visualization

Sequence design and software environment for real-time navigation of a wireless ferromagnetic device using MRI system and single echo 3D tracking.

PubMed

Chanu, A; Aboussouan, E; Tamaz, S; Martel, S

2006-01-01

Software architecture for the navigation of a ferromagnetic untethered device in a 1D and 2D phantom environment is briefly described. Navigation is achieved using the real-time capabilities of a Siemens 1.5 T Avanto MRI system coupled with a dedicated software environment and a specially developed 3D tracking pulse sequence. Real-time control of the magnetic core is executed through the implementation of a simple PID controller. 1D and 2D experimental results are presented.

A real-time PCR diagnostic method for detection of Naegleria fowleri.

PubMed

Madarová, Lucia; Trnková, Katarína; Feiková, Sona; Klement, Cyril; Obernauerová, Margita

2010-09-01

Naegleria fowleri is a free-living amoeba that can cause primary amoebic meningoencephalitis (PAM). While, traditional methods for diagnosing PAM still rely on culture, more current laboratory diagnoses exist based on conventional PCR methods; however, only a few real-time PCR processes have been described as yet. Here, we describe a real-time PCR-based diagnostic method using hybridization fluorescent labelled probes, with a LightCycler instrument and accompanying software (Roche), targeting the Naegleria fowleriMp2Cl5 gene sequence. Using this method, no cross reactivity with other tested epidemiologically relevant prokaryotic and eukaryotic organisms was found. The reaction detection limit was 1 copy of the Mp2Cl5 DNA sequence. This assay could become useful in the rapid laboratory diagnostic assessment of the presence or absence of Naegleria fowleri. Copyright 2009 Elsevier Inc. All rights reserved.

Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation

PubMed Central

Jackson, Brendan R.; Tarr, Cheryl; Strain, Errol; Jackson, Kelly A.; Conrad, Amanda; Carleton, Heather; Katz, Lee S.; Stroika, Steven; Gould, L. Hannah; Mody, Rajal K.; Silk, Benjamin J.; Beal, Jennifer; Chen, Yi; Timme, Ruth; Doyle, Matthew; Fields, Angela; Wise, Matthew; Tillman, Glenn; Defibaugh-Chavez, Stephanie; Kucerova, Zuzana; Sabol, Ashley; Roache, Katie; Trees, Eija; Simmons, Mustafa; Wasilenko, Jamie; Kubota, Kristy; Pouseele, Hannes; Klimke, William; Besser, John; Brown, Eric; Allard, Marc; Gerner-Smidt, Peter

2016-01-01

Listeria monocytogenes (Lm) causes severe foodborne illness (listeriosis). Previous molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE), were critical in detecting outbreaks that led to food safety improvements and declining incidence, but PFGE provides limited genetic resolution. A multiagency collaboration began performing real-time, whole-genome sequencing (WGS) on all US Lm isolates from patients, food, and the environment in September 2013, posting sequencing data into a public repository. Compared with the year before the project began, WGS, combined with epidemiologic and product trace-back data, detected more listeriosis clusters and solved more outbreaks (2 outbreaks in pre-WGS year, 5 in WGS year 1, and 9 in year 2). Whole-genome multilocus sequence typing and single nucleotide polymorphism analyses provided equivalent phylogenetic relationships relevant to investigations; results were most useful when interpreted in context of epidemiological data. WGS has transformed listeriosis outbreak surveillance and is being implemented for other foodborne pathogens. PMID:27090985

Software algorithm and hardware design for real-time implementation of new spectral estimator

PubMed Central

2014-01-01

Background Real-time spectral analyzers can be difficult to implement for PC computer-based systems because of the potential for high computational cost, and algorithm complexity. In this work a new spectral estimator (NSE) is developed for real-time analysis, and compared with the discrete Fourier transform (DFT). Method Clinical data in the form of 216 fractionated atrial electrogram sequences were used as inputs. The sample rate for acquisition was 977 Hz, or approximately 1 millisecond between digital samples. Real-time NSE power spectra were generated for 16,384 consecutive data points. The same data sequences were used for spectral calculation using a radix-2 implementation of the DFT. The NSE algorithm was also developed for implementation as a real-time spectral analyzer electronic circuit board. Results The average interval for a single real-time spectral calculation in software was 3.29 μs for NSE versus 504.5 μs for DFT. Thus for real-time spectral analysis, the NSE algorithm is approximately 150× faster than the DFT. Over a 1 millisecond sampling period, the NSE algorithm had the capability to spectrally analyze a maximum of 303 data channels, while the DFT algorithm could only analyze a single channel. Moreover, for the 8 second sequences, the NSE spectral resolution in the 3-12 Hz range was 0.037 Hz while the DFT spectral resolution was only 0.122 Hz. The NSE was also found to be implementable as a standalone spectral analyzer board using approximately 26 integrated circuits at a cost of approximately $500. The software files used for analysis are included as a supplement, please see the Additional files 1 and 2. Conclusions The NSE real-time algorithm has low computational cost and complexity, and is implementable in both software and hardware for 1 millisecond updates of multichannel spectra. The algorithm may be helpful to guide radiofrequency catheter ablation in real time. PMID:24886214

Impact of scatterometer wind (ASCAT-A/B) data assimilation on semi real-time forecast system at KIAPS

NASA Astrophysics Data System (ADS)

Han, H. J.; Kang, J. H.

2016-12-01

Since Jul. 2015, KIAPS (Korea Institute of Atmospheric Prediction Systems) has been performing the semi real-time forecast system to assess the performance of their forecast system as a NWP model. KPOP (KIAPS Protocol for Observation Processing) is a part of KIAPS data assimilation system and has been performing well in KIAPS semi real-time forecast system. In this study, due to the fact that KPOP would be able to treat the scatterometer wind data, we analyze the effect of scatterometer wind (ASCAT-A/B) on KIAPS semi real-time forecast system. O-B global distribution and statistics of scatterometer wind give use two information which are the difference between background field and observation is not too large and KPOP processed the scatterometer wind data well. The changes of analysis increment because of O-B global distribution appear remarkably at the bottom of atmospheric field. It also shows that scatterometer wind data cover wide ocean where data would be able to short. Performance of scatterometer wind data can be checked through the vertical error reduction against IFS between background and analysis field and vertical statistics of O-A. By these analysis result, we can notice that scatterometer wind data will influence the positive effect on lower level performance of semi real-time forecast system at KIAPS. After, long-term result based on effect of scatterometer wind data will be analyzed.

Pick- and waveform-based techniques for real-time detection of induced seismicity

NASA Astrophysics Data System (ADS)

Grigoli, Francesco; Scarabello, Luca; Böse, Maren; Weber, Bernd; Wiemer, Stefan; Clinton, John F.

2018-05-01

The monitoring of induced seismicity is a common operation in many industrial activities, such as conventional and non-conventional hydrocarbon production or mining and geothermal energy exploitation, to cite a few. During such operations, we generally collect very large and strongly noise-contaminated data sets that require robust and automated analysis procedures. Induced seismicity data sets are often characterized by sequences of multiple events with short interevent times or overlapping events; in these cases, pick-based location methods may struggle to correctly assign picks to phases and events, and errors can lead to missed detections and/or reduced location resolution and incorrect magnitudes, which can have significant consequences if real-time seismicity information are used for risk assessment frameworks. To overcome these issues, different waveform-based methods for the detection and location of microseismicity have been proposed. The main advantages of waveform-based methods is that they appear to perform better and can simultaneously detect and locate seismic events providing high-quality locations in a single step, while the main disadvantage is that they are computationally expensive. Although these methods have been applied to different induced seismicity data sets, an extensive comparison with sophisticated pick-based detection methods is still missing. In this work, we introduce our improved waveform-based detector and we compare its performance with two pick-based detectors implemented within the SeiscomP3 software suite. We test the performance of these three approaches with both synthetic and real data sets related to the induced seismicity sequence at the deep geothermal project in the vicinity of the city of St. Gallen, Switzerland.

A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus.

PubMed

Kang, Xiao-ping; Jiang, Tao; Li, Yong-qiang; Lin, Fang; Liu, Hong; Chang, Guo-hui; Zhu, Qing-yu; Qin, E-de; Qin, Cheng-feng; Yang, Yin-hui

2010-06-02

A duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was improved for simultaneous detection of highly pathogenic H5N1 avian influenza virus and pandemic H1N1 (2009) influenza virus, which is suitable for early diagnosis of influenza-like patients and for epidemiological surveillance. The sensitivity of this duplex real-time RT-PCR assay was 0.02 TCID50 (50% tissue culture infective dose) for H5N1 and 0.2 TCID50 for the pandemic H1N1, which was the same as that of each single-target RT-PCR for pandemic H1N1 and even more sensitive for H5N1 with the same primers and probes. No cross reactivity of detecting other subtype influenza viruses or respiratory tract viruses was observed. Two hundred and thirty-six clinical specimens were tested by comparing with single real-time RT-PCR and result from the duplex assay was 100% consistent with the results of single real-time RT-PCR and sequence analysis.

Graph-based real-time fault diagnostics

NASA Technical Reports Server (NTRS)

Padalkar, S.; Karsai, G.; Sztipanovits, J.

1988-01-01

A real-time fault detection and diagnosis capability is absolutely crucial in the design of large-scale space systems. Some of the existing AI-based fault diagnostic techniques like expert systems and qualitative modelling are frequently ill-suited for this purpose. Expert systems are often inadequately structured, difficult to validate and suffer from knowledge acquisition bottlenecks. Qualitative modelling techniques sometimes generate a large number of failure source alternatives, thus hampering speedy diagnosis. In this paper we present a graph-based technique which is well suited for real-time fault diagnosis, structured knowledge representation and acquisition and testing and validation. A Hierarchical Fault Model of the system to be diagnosed is developed. At each level of hierarchy, there exist fault propagation digraphs denoting causal relations between failure modes of subsystems. The edges of such a digraph are weighted with fault propagation time intervals. Efficient and restartable graph algorithms are used for on-line speedy identification of failure source components.

Competitive On-Line Scheduling for Overloaded Real-Time Systems

DTIC Science & Technology

1993-09-01

Real - Time Systems by Gilad Koren a dissertation submitted in partial fulfillment of the requirements...Overloaded Real - Time Systems 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK...1.1 Introduction : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 2 1.1.1 Real - Time Systems : : : : : : : : : : : : : : : : : : : : : : : : : : : :

Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array

PubMed Central

Fuller, Carl W.; Kumar, Shiv; Porel, Mintu; Chien, Minchen; Bibillo, Arek; Stranges, P. Benjamin; Dorwart, Michael; Tao, Chuanjuan; Li, Zengmin; Guo, Wenjing; Shi, Shundi; Korenblum, Daniel; Trans, Andrew; Aguirre, Anne; Liu, Edward; Harada, Eric T.; Pollard, James; Bhat, Ashwini; Cech, Cynthia; Yang, Alexander; Arnold, Cleoma; Palla, Mirkó; Hovis, Jennifer; Chen, Roger; Morozova, Irina; Kalachikov, Sergey; Russo, James J.; Kasianowicz, John J.; Davis, Randy; Roever, Stefan; Church, George M.; Ju, Jingyue

2016-01-01

DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5′-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time single-molecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods. PMID:27091962

Real-time micro-vibration multi-spot synchronous measurement within a region based on heterodyne interference

NASA Astrophysics Data System (ADS)

Lan, Ma; Xiao, Wen; Chen, Zonghui; Hao, Hongliang; Pan, Feng

2018-01-01

Real-time micro-vibration measurement is widely used in engineering applications. It is very difficult for traditional optical detection methods to achieve real-time need in a relatively high frequency and multi-spot synchronous measurement of a region at the same time,especially at the nanoscale. Based on the method of heterodyne interference, an experimental system of real-time measurement of micro - vibration is constructed to satisfy the demand in engineering applications. The vibration response signal is measured by combing optical heterodyne interferometry and a high-speed CMOS-DVR image acquisition system. Then, by extracting and processing multiple pixels at the same time, four digital demodulation technique are implemented to simultaneously acquire the vibrating velocity of the target from the recorded sequences of images. Different kinds of demodulation algorithms are analyzed and the results show that these four demodulation algorithms are suitable for different interference signals. Both autocorrelation algorithm and cross-correlation algorithm meet the needs of real-time measurements. The autocorrelation algorithm demodulates the frequency more accurately, while the cross-correlation algorithm is more accurate in solving the amplitude.

Design and implementation of real-time wireless projection system based on ARM embedded system

NASA Astrophysics Data System (ADS)

Long, Zhaohua; Tang, Hao; Huang, Junhua

2018-04-01

Aiming at the shortage of existing real-time screen sharing system, a real-time wireless projection system is proposed in this paper. Based on the proposed system, a weight-based frame deletion strategy combined sampling time period and data variation is proposed. By implementing the system on the hardware platform, the results show that the system can achieve good results. The weight-based strategy can improve the service quality, reduce the delay and optimize the real-time customer service system [1].

GPU-Based Real-Time Volumetric Ultrasound Image Reconstruction for a Ring Array

PubMed Central

Choe, Jung Woo; Nikoozadeh, Amin; Oralkan, Ömer; Khuri-Yakub, Butrus T.

2014-01-01

Synthetic phased array (SPA) beamforming with Hadamard coding and aperture weighting is an optimal option for real-time volumetric imaging with a ring array, a particularly attractive geometry in intracardiac and intravascular applications. However, the imaging frame rate of this method is limited by the immense computational load required in synthetic beamforming. For fast imaging with a ring array, we developed graphics processing unit (GPU)-based, real-time image reconstruction software that exploits massive data-level parallelism in beamforming operations. The GPU-based software reconstructs and displays three cross-sectional images at 45 frames per second (fps). This frame rate is 4.5 times higher than that for our previously-developed multi-core CPU-based software. In an alternative imaging mode, it shows one B-mode image rotating about the axis and its maximum intensity projection (MIP), processed at a rate of 104 fps. This paper describes the image reconstruction procedure on the GPU platform and presents the experimental images obtained using this software. PMID:23529080

Recurrent high level parvovirus B19/genotype 2 viremia in a renal transplant recipient analyzed by real-time PCR for simultaneous detection of genotypes 1 to 3.

PubMed

Liefeldt, Lutz; Plentz, Annelie; Klempa, Boris; Kershaw, Olivia; Endres, Anne-Sophie; Raab, Ulla; Neumayer, Hans-H; Meisel, Helga; Modrow, Susanne

2005-01-01

Organ transplant recipients infected with parvovirus B19 frequently develop persistent viremia associated with chronic anemia and pure red cell aplasia. In this study, a male renal transplant recipient who had been infected with parvovirus B19/genotype 2 after renal transplantation at the age of 34 years is described. The patient was repeatedly treated with high dose intravenous immunoglobulin (IVIG) that resulted in the resolvement of symptoms but not in virus eradication. During an observation period of 33 months after transplantation three phases associated with high parvovirus B19 viremia were observed. Both the first and the second viremic phases were combined with severe anemia. Parvovirus B19 specific IgM-antibodies were initially detected at the beginning of the second phase in continually rising concentrations. Initially eradication of the virus by immunoglobulin therapy was reported after the first viremic phase [Liefeldt et al. (2002): Nephrol Dial Transplant 17:1840-1842]. Retrospectively this statement has to be corrected. It was based on the use of a qualitative PCR assay specific for parvovirus B19 genotype 1 associated with reduced sensitivity for detection of genotype 2. After sequence analysis of the viral DNA and adjustment of a real-time PCR assay (TaqMan) for quantitative detection of all three B19 virus genotypes analysis of consecutive serum samples allowed the demonstration of long lasting phases with reduced viral loads following IVIG-treatment. These results demonstrate that IVIG treatment of parvovirus B19-triggered anemia in transplant recipients offers an opportunity to resolve symptoms, but does not guarantee eradication of the virus. Since reactivation of parvovirus B19 infection can result in high virus load associated with the recurrence of symptoms repeated screening for viral DNA is recommended using the TaqMan system established for quantitative detection of all three genotypes of parvovirus B19. Copyright 2005 Wiley-Liss, Inc.

Development and Evaluation of Novel Real-Time Reverse Transcription-PCR Assays with Locked Nucleic Acid Probes Targeting Leader Sequences of Human-Pathogenic Coronaviruses

PubMed Central

Chan, Jasper Fuk-Woo; Choi, Garnet Kwan-Yue; Tsang, Alan Ka-Lun; Tee, Kah-Meng; Lam, Ho-Yin; Yip, Cyril Chik-Yan; To, Kelvin Kai-Wang; Cheng, Vincent Chi-Chung; Yeung, Man-Lung; Lau, Susanna Kar-Pui; Woo, Patrick Chiu-Yat; Chan, Kwok-Hung; Tang, Bone Siu-Fai

2015-01-01

Based on findings in small RNA-sequencing (Seq) data analysis, we developed highly sensitive and specific real-time reverse transcription (RT)-PCR assays with locked nucleic acid probes targeting the abundantly expressed leader sequences of Middle East respiratory syndrome coronavirus (MERS-CoV) and other human coronaviruses. Analytical and clinical evaluations showed their noninferiority to a commercial multiplex PCR test for the detection of these coronaviruses. PMID:26019210

Real-time Kp predictions from ACE real time solar wind

NASA Astrophysics Data System (ADS)

Detman, Thomas; Joselyn, Joann

1999-06-01

The Advanced Composition Explorer (ACE) spacecraft provides nearly continuous monitoring of solar wind plasma, magnetic fields, and energetic particles from the Sun-Earth L1 Lagrange point upstream of Earth in the solar wind. The Space Environment Center (SEC) in Boulder receives ACE telemetry from a group of international network of tracking stations. One-minute, and 1-hour averages of solar wind speed, density, temperature, and magnetic field components are posted on SEC's World Wide Web page within 3 to 5 minutes after they are measured. The ACE Real Time Solar Wind (RTSW) can be used to provide real-time warnings and short term forecasts of geomagnetic storms based on the (traditional) Kp index. Here, we use historical data to evaluate the performance of the first real-time Kp prediction algorithm to become operational.

Effect of Above Real Time Training and Post Flight Feedback in Training of Novice Pilots in a PC-Based Flight Simulator

NASA Technical Reports Server (NTRS)

Khan, M. Javed; Rossi, Marcia; Heath, Bruce E.; Ali, Syed firasat; Crane, Peter; Knighten, Tremaine; Culpepper, Christi

2003-01-01

The use of Post-Flight Feedback (PFFB) and Above Real-Time Training (ARTT) while training novice pilots to perform a coordinated level turn on a PC-based flight simulator was investigated. One group trained at 1.5 ARTT followed by an equal number of flights at 2.0 ARTT; the second group experienced Real Time Training (RTT). The total number of flights for both groups was equal. Each group was further subdivided into two groups one of which was provided PFFB while the other was not. Then, all participants experienced two challenging evaluation missions in real time. Performance was assessed by comparing root-mean-square error in bank-angle and altitude. Participants in the 1.512.0 ARTT No-PFFB sequence did not show improvement in performance across training sessions. An ANOVA on performance in evaluation flights found that the PFFB groups performed significantly better than those with No-PFFB. Also, the RTT groups performed significantly better than the ARTT groups. Data from two additional groups trained under a 2.011.5 ARTT PFFB and No-PFFB regimes were collected and combined with data from the previously Trainers, Real-time simulation, Personal studied groups and reanalyzed to study the computers, Man-in-the-loop simulation influence of sequence. An ANOVA on test trials found no significant effects between groups. Under training situations involving ARTT we recommend that appropriate PFFB be provided.

Flexible real-time magnetic resonance imaging framework.

PubMed

Santos, Juan M; Wright, Graham A; Pauly, John M

2004-01-01

The extension of MR imaging to new applications has demonstrated the limitations of the architecture of current real-time systems. Traditional real-time implementations provide continuous acquisition of data and modification of basic sequence parameters on the fly. We have extended the concept of real-time MRI by designing a system that drives the examinations from a real-time localizer and then gets reconfigured for different imaging modes. Upon operator request or automatic feedback the system can immediately generate a new pulse sequence or change fundamental aspects of the acquisition such as gradient waveforms excitation pulses and scan planes. This framework has been implemented by connecting a data processing and control workstation to a conventional clinical scanner. Key components on the design of this framework are the data communication and control mechanisms, reconstruction algorithms optimized for real-time and adaptability, flexible user interface and extensible user interaction. In this paper we describe the various components that comprise this system. Some of the applications implemented in this framework include real-time catheter tracking embedded in high frame rate real-time imaging and immediate switching between real-time localizer and high-resolution volume imaging for coronary angiography applications.

FPGA-based real-time swept-source OCT systems for B-scan live-streaming or volumetric imaging

NASA Astrophysics Data System (ADS)

Bandi, Vinzenz; Goette, Josef; Jacomet, Marcel; von Niederhäusern, Tim; Bachmann, Adrian H.; Duelk, Marcus

2013-03-01

We have developed a Swept-Source Optical Coherence Tomography (Ss-OCT) system with high-speed, real-time signal processing on a commercially available Data-Acquisition (DAQ) board with a Field-Programmable Gate Array (FPGA). The Ss-OCT system simultaneously acquires OCT and k-clock reference signals at 500MS/s. From the k-clock signal of each A-scan we extract a remap vector for the k-space linearization of the OCT signal. The linear but oversampled interpolation is followed by a 2048-point FFT, additional auxiliary computations, and a data transfer to a host computer for real-time, live-streaming of B-scan or volumetric C-scan OCT visualization. We achieve a 100 kHz A-scan rate by parallelization of our hardware algorithms, which run on standard and affordable, commercially available DAQ boards. Our main development tool for signal analysis as well as for hardware synthesis is MATLAB® with add-on toolboxes and 3rd-party tools.

Detection of adulterated murine components in meat products by TaqMan© real-time PCR.

PubMed

Fang, Xin; Zhang, Chi

2016-02-01

Using murine meat to substitute mutton has been identified as a new type of meat fraud in China, yet no detection method for murine species has been reported. Here, three kinds of rodent were used as target species to establish a murine-specific real-time PCR method of detection. The mitochondrial cytochrome b gene (cytb) of each target was sequenced and a TaqMan probe was designed based on the cytb. Simultaneously, an internal positive control (IPC) plasmid along with its respective probe were designed to monitor the PCR reaction. As a result, the duplex real-time PCR system was verified to be specific. The limit of detection (LOD) was lower than 1 pg of DNA per reaction and 0.1% murine contamination in meat mixtures. Standard curves were generated for a quantitative analysis. Thus, this study provided a new tool to control the quality of meat products for official and third-party laboratories. Copyright © 2015. Published by Elsevier Ltd.

A real-time MTFC algorithm of space remote-sensing camera based on FPGA

NASA Astrophysics Data System (ADS)

Zhao, Liting; Huang, Gang; Lin, Zhe

2018-01-01

A real-time MTFC algorithm of space remote-sensing camera based on FPGA was designed. The algorithm can provide real-time image processing to enhance image clarity when the remote-sensing camera running on-orbit. The image restoration algorithm adopted modular design. The MTF measurement calculation module on-orbit had the function of calculating the edge extension function, line extension function, ESF difference operation, normalization MTF and MTFC parameters. The MTFC image filtering and noise suppression had the function of filtering algorithm and effectively suppressing the noise. The algorithm used System Generator to design the image processing algorithms to simplify the design structure of system and the process redesign. The image gray gradient dot sharpness edge contrast and median-high frequency were enhanced. The image SNR after recovery reduced less than 1 dB compared to the original image. The image restoration system can be widely used in various fields.

Internal control for real-time polymerase chain reaction based on MS2 bacteriophage for RNA viruses diagnostics.

PubMed

Zambenedetti, Miriam Ribas; Pavoni, Daniela Parada; Dallabona, Andreia Cristine; Dominguez, Alejandro Correa; Poersch, Celina de Oliveira; Fragoso, Stenio Perdigão; Krieger, Marco Aurélio

2017-05-01

Real-time reverse transcription polymerase chain reaction (RT-PCR) is routinely used to detect viral infections. In Brazil, it is mandatory the use of nucleic acid tests to detect hepatitis C virus (HCV), hepatitis B virus and human immunodeficiency virus in blood banks because of the immunological window. The use of an internal control (IC) is necessary to differentiate the true negative results from those consequent from a failure in some step of the nucleic acid test. The aim of this study was the construction of virus-modified particles, based on MS2 bacteriophage, to be used as IC for the diagnosis of RNA viruses. The MS2 genome was cloned into the pET47b(+) plasmid, generating pET47b(+)-MS2. MS2-like particles were produced through the synthesis of MS2 RNA genome by T7 RNA polymerase. These particles were used as non-competitive IC in assays for RNA virus diagnostics. In addition, a competitive control for HCV diagnosis was developed by cloning a mutated HCV sequence into the MS2 replicase gene of pET47b(+)-MS2, which produces a non-propagating MS2 particle. The utility of MS2-like particles as IC was evaluated in a one-step format multiplex real-time RT-PCR for HCV detection. We demonstrated that both competitive and non-competitive IC could be successfully used to monitor the HCV amplification performance, including the extraction, reverse transcription, amplification and detection steps, without compromising the detection of samples with low target concentrations. In conclusion, MS2-like particles generated by this strategy proved to be useful IC for RNA virus diagnosis, with advantage that they are produced by a low cost protocol. An attractive feature of this system is that it allows the construction of a multicontrol by the insertion of sequences from more than one pathogen, increasing its applicability for diagnosing different RNA viruses.

Internal control for real-time polymerase chain reaction based on MS2 bacteriophage for RNA viruses diagnostics

PubMed Central

Zambenedetti, Miriam Ribas; Pavoni, Daniela Parada; Dallabona, Andreia Cristine; Dominguez, Alejandro Correa; Poersch, Celina de Oliveira; Fragoso, Stenio Perdigão; Krieger, Marco Aurélio

2017-01-01

BACKGROUND Real-time reverse transcription polymerase chain reaction (RT-PCR) is routinely used to detect viral infections. In Brazil, it is mandatory the use of nucleic acid tests to detect hepatitis C virus (HCV), hepatitis B virus and human immunodeficiency virus in blood banks because of the immunological window. The use of an internal control (IC) is necessary to differentiate the true negative results from those consequent from a failure in some step of the nucleic acid test. OBJECTIVES The aim of this study was the construction of virus-modified particles, based on MS2 bacteriophage, to be used as IC for the diagnosis of RNA viruses. METHODS The MS2 genome was cloned into the pET47b(+) plasmid, generating pET47b(+)-MS2. MS2-like particles were produced through the synthesis of MS2 RNA genome by T7 RNA polymerase. These particles were used as non-competitive IC in assays for RNA virus diagnostics. In addition, a competitive control for HCV diagnosis was developed by cloning a mutated HCV sequence into the MS2 replicase gene of pET47b(+)-MS2, which produces a non-propagating MS2 particle. The utility of MS2-like particles as IC was evaluated in a one-step format multiplex real-time RT-PCR for HCV detection. FINDINGS We demonstrated that both competitive and non-competitive IC could be successfully used to monitor the HCV amplification performance, including the extraction, reverse transcription, amplification and detection steps, without compromising the detection of samples with low target concentrations. In conclusion, MS2-like particles generated by this strategy proved to be useful IC for RNA virus diagnosis, with advantage that they are produced by a low cost protocol. An attractive feature of this system is that it allows the construction of a multicontrol by the insertion of sequences from more than one pathogen, increasing its applicability for diagnosing different RNA viruses. PMID:28403327

Real-time global illumination on mobile device

NASA Astrophysics Data System (ADS)

Ahn, Minsu; Ha, Inwoo; Lee, Hyong-Euk; Kim, James D. K.

2014-02-01

We propose a novel method for real-time global illumination on mobile devices. Our approach is based on instant radiosity, which uses a sequence of virtual point lights in order to represent the e ect of indirect illumination. Our rendering process consists of three stages. With the primary light, the rst stage generates a local illumination with the shadow map on GPU The second stage of the global illumination uses the re ective shadow map on GPU and generates the sequence of virtual point lights on CPU. Finally, we use the splatting method of Dachsbacher et al 1 and add the indirect illumination to the local illumination on GPU. With the limited computing resources in mobile devices, a small number of virtual point lights are allowed for real-time rendering. Our approach uses the multi-resolution sampling method with 3D geometry and attributes simultaneously and reduce the total number of virtual point lights. We also use the hybrid strategy, which collaboratively combines the CPUs and GPUs available in a mobile SoC due to the limited computing resources in mobile devices. Experimental results demonstrate the global illumination performance of the proposed method.

Multiplex real-time PCR assay for Legionella species.

PubMed

Kim, Seung Min; Jeong, Yoojung; Sohn, Jang Wook; Kim, Min Ja

2015-12-01

Legionella pneumophila serogroup 1 (sg1) accounts for the majority of infections in humans, but other Legionella species are also associated with human disease. In this study, a new SYBR Green I-based multiplex real-time PCR assay in a single reaction was developed to allow the rapid detection and differentiation of Legionella species by targeting specific gene sequences. Candidate target genes were selected, and primer sets were designed by referring to comparative genomic hybridization data of Legionella species. The Legionella species-specific groES primer set successfully detected all 30 Legionella strains tested. The xcpX and rfbA primers specifically detected L. pneumophila sg1-15 and L. pneumophila sg1, respectively. In addition, this assay was validated by testing clinical samples and isolates. In conclusion, this novel multiplex real-time PCR assay might be a useful diagnostic tool for the rapid detection and differentiation of Legionella species in both clinical and epidemiological studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identification of Microbial Profile of Koji Using Single Molecule, Real-Time Sequencing Technology.

PubMed

Hui, Wenyan; Hou, Qiangchuan; Cao, Chenxia; Xu, Haiyan; Zhen, Yi; Kwok, Lai-Yu; Sun, Tiansong; Zhang, Heping; Zhang, Wenyi

2017-05-01

Koji is a kind of Japanese traditional fermented starter that has been used for centuries. Many fermented foods are made from koji, such as sake, miso, and soy sauce. This study used the single molecule real-time sequencing technology (SMRT) to investigate the bacterial and fungal microbiota of 3 Japanese koji samples. After SMRT analysis, a total of 39121 high-quality sequences were generated, including 14354 bacterial and 24767 fungal sequence reads. The high-quality gene sequences were assigned to 5 bacterial and 2 fungal plyla, dominated by Proteobacteria and Ascomycota, respectively. At the genus level, Ochrobactrum and Wickerhamomyces were the most abundant bacterial and fungal genera, respectively. The predominant bacterial and fungal species were Ochrobactrum lupini and Wickerhamomyces anomalus, respectively. Our study profiled the microbiota composition of 3 Japanese koji samples to the species level precision. The results may be useful for further development of traditional fermented products, especially optimization of koji preparation. Meanwhile, this study has demonstrated that SMRT is a robust tool for analyzing the microbial composition in food samples. © 2017 Institute of Food Technologists®.

Critical (of) Issues in Real-Time Systems.

DTIC Science & Technology

1988-05-03

IACCESON 11 T IT LE (Include Security Classification) Cr it ic, (of) issues in real .- time systems A Position Paper 12 PERPSONAL AU THOR(S) Fr ed B...are obsolete %0%’ 4.’.C %" Critical (of) issues in real - time systems ’ • "A Position Paper Acc, son For NTIS R& DTrC TAB May 3, 1988 Uyjannotuce~d...m . 2C:. r Ithaca, New York 14853 Dist 1 -.1 g- It is time to place the development of real - time systems on a firm scientific basis. Unlike other

Evaluation of the Persistence of Infectious Human Noroviruses on Food Surfaces by Using Real-Time Nucleic Acid Sequence-Based Amplification▿

PubMed Central

Lamhoujeb, Safaa; Fliss, Ismail; Ngazoa, Solange E.; Jean, Julie

2008-01-01

Noroviruses (NoV) are the major cause of nonbacterial gastroenteritis. However, there is no published study to ascertain their survival on foodstuffs which are directly related to human health risk. In the present study, we developed a rapid, simple, and sensitive real-time nucleic acid sequence-based amplification (NASBA) combined with an enzymatic treatment for distinguishing infectious from noninfectious human NoV. The developed method was validated using spiked ready-to-eat food samples. When feline calicivirus (FCV) was used as a NoV surrogate in the preliminary assays, it appeared more sensitive to heat inactivation and enzymatic pretreatment than the human NoV. This suggests that FCV may not be an ideal model for studying NoV. Our results reveal clearly that the developed enzymatic pretreatment/real-time NASBA combination successfully distinguished the infectious from heat-inactivated NoV. Moreover, we demonstrate that NoV survived for at least 10 days on refrigerated ready-to-eat foods, such as lettuce and turkey. However, the survival rate was higher on turkey than on lettuce, probably because of their different surface natures. The approach developed in this study may be suitable for more in-depth studies of the persistence and inactivation of human NoV and may be applied to other nonculturable RNA viruses. Moreover, the evaluation of infectious NoV survival provided valuable information concerning its persistence on ready-to-eat food. PMID:18378643

Frequency Based Real-time Pricing for Residential Prosumers

NASA Astrophysics Data System (ADS)

Hambridge, Sarah Mabel

This work is the first to explore frequency based pricing for secondary frequency control as a price-reactive control mechanism for residential prosumers. A frequency based real-time electricity rate is designed as an autonomous market control mechanism for residential prosumers to provide frequency support as an ancillary service. In addition, prosumers are empowered to participate in dynamic energy transactions, therefore integrating Distributed Energy Resources (DERs), and increasing distributed energy storage onto the distributed grid. As the grid transitions towards DERs, a new market based control system will take the place of the legacy distributed system and possibly the legacy bulk power system. DERs provide many benefits such as energy independence, clean generation, efficiency, and reliability to prosumers during blackouts. However, the variable nature of renewable energy and current lack of installed energy storage on the grid will create imbalances in supply and demand as uptake increases, affecting the grid frequency and system operation. Through a frequency-based electricity rate, prosumers will be encouraged to purchase energy storage systems (ESS) to offset their neighbor's distributed generation (DG) such as solar. Chapter 1 explains the deregulation of the power system and move towards Distributed System Operators (DSOs), as prosumers become owners of microgrids and energy cells connected to the distributed system. Dynamic pricing has been proposed as a benefit to prosumers, giving them the ability to make decisions in the energy market, while also providing a way to influence and control their behavior. Frequency based real-time pricing is a type of dynamic pricing which falls between price-reactive control and transactive control. Prosumer-to-prosumer transactions may take the place of prosumer-to-utility transactions, building The Energy Internet. Frequency based pricing could be a mechanism for determining prosumer prices and supporting

Ground-based real-time tracking and traverse recovery of China's first lunar rover

NASA Astrophysics Data System (ADS)

Zhou, Huan; Li, Haitao; Xu, Dezhen; Dong, Guangliang

2016-02-01

The Chang'E-3 unmanned lunar exploration mission forms an important stage in China's Lunar Exploration Program. China's first lunar rover "Yutu" is a sub-probe of the Chang'E-3 mission. Its main science objectives cover the investigations of the lunar soil and crust structure, explorations of mineral resources, and analyses of matter compositions. Some of these tasks require accurate real-time and continuous position tracking of the rover. To achieve these goals with the scale-limited Chinese observation network, this study proposed a ground-based real-time very long baseline interferometry phase referencing tracking method. We choose the Chang'E-3 lander as the phase reference source, and the accurate location of the rover is updated every 10 s using its radio-image sequences with the help of a priori information. The detailed movements of the Yutu rover have been captured with a sensitivity of several centimeters, and its traverse across the lunar surface during the first few days after its separation from the Chang'E-3 lander has been recovered. Comparisons and analysis show that the position tracking accuracy reaches a 1-m level.

Detection of Histoplasma capsulatum from clinical specimens by cycling probe-based real-time PCR and nested real-time PCR.

PubMed

Muraosa, Yasunori; Toyotome, Takahito; Yahiro, Maki; Watanabe, Akira; Shikanai-Yasuda, Maria Aparecida; Kamei, Katsuhiko

2016-05-01

We developed new cycling probe-based real-time PCR and nested real-time PCR assays for the detection of Histoplasma capsulatum that were designed to detect the gene encoding N-acetylated α-linked acidic dipeptidase (NAALADase), which we previously identified as an H. capsulatum antigen reacting with sera from patients with histoplasmosis. Both assays specifically detected the DNAs of all H. capsulatum strains but not those of other fungi or human DNA. The limited of detection (LOD) of the real-time PCR assay was 10 DNA copies when using 10-fold serial dilutions of the standard plasmid DNA and 50 DNA copies when using human serum spiked with standard plasmid DNA. The nested real-time PCR improved the LOD to 5 DNA copies when using human serum spiked with standard plasmid DNA, which represents a 10-fold higher than that observed with the real-time PCR assay. To assess the ability of the two assays to diagnose histoplasmosis, we analyzed a small number of clinical specimens collected from five patients with histoplasmosis, such as sera (n = 4), formalin-fixed paraffin-embedded (FFPE) tissue (n = 4), and bronchoalveolar lavage fluid (BALF) (n = 1). Although clinical sensitivity of the real-time PCR assay was insufficiently sensitive (33%), the nested real-time PCR assay increased the clinical sensitivity (77%), suggesting it has a potential to be a useful method for detecting H. capsulatum DNA in clinical specimens. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Real-time Monitoring of Nanoparticle-based Therapeutics: A Review.

PubMed

Han, Qingqing; Niu, Meng; Wu, Qirun; Zhong, Hongshan

2018-01-01

With the development of nanomaterials, nanoparticle-based therapeutics have found increasing application in various fields, including clinical and basic medicine. Real-time monitoring of nanoparticle-based therapeutics is considered critical to both pharmacology and pharmacokinetics. In this review, we discuss the different methods of real-time monitoring of nanoparticle-based therapeutics comprising different types of nanoparticle carriers, such as metal nanoparticles, inorganic nonmetallic nanoparticles, biodegradable polymer nanoparticles, and biological nanoparticles. In the light of examples and analyses, we conclude that the methods of analysis of the four types of nanoparticle carriers are commonly used methods and mostly not necessary. Under most circumstances, real-time monitoring differs according to nanoparticle type, drugs, diseases, and surroundings. With technology development and advanced researches, there have been increasing measures to track the real-time changes in nanoparticles, and this has led to great progress in pharmacology and therapeutics. However, future studies are warranted to determine the accuracy, applicability, and practicability of different technologies. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

FY*X real-time polymerase chain reaction with melting curve analysis associated with a complete one-step real-time FY genotyping.

PubMed

Ansart-Pirenne, H; Martin-Blanc, S; Le Pennec, P-Y; Rouger, P; Cartron, J-P; Tournamille, C

2007-02-01

The Duffy (FY) blood group system is controlled by four major alleles: FY*A and FY*B, the Caucasian common alleles, encoding Fy(a) and Fy(b) antigens; FY*X allele responsible for a poorly expressed Fy(b) antigen, and FY*Fy a silent predominant allele among Black population. Despite the recent development of a real-time fluorescent polymerase chain reaction (PCR) method for FY genotyping FY*X genotyping has not been described by this method. This study focused on the real-time FY*X genotyping development associated with a complete, one-step real-time FY genotyping, based on fluorescence resonance energy transfer (FRET) technology. Seventy-two blood samples from Fy(a+b-) Caucasian blood donors were studied by real-time PCR only. Forty-seven Caucasian and Black individual blood samples, referred to our laboratory, were studied by PCR-RFLP and real-time PCR. For each individual, the result of the genotype was compared to the known phenotype. The FY*X allele frequency calculated in an Fy(a+b-) Caucasian blood donors population was 0.014. With the Caucasian and Black patient samples we found a complete correlation between PCR-RFLP and the real-time PCR method whatever the alleles combination tested. When the known phenotype was not correlated to FY*X genotype, the presence of the Fy(b) antigen was always confirmed by adsorption-elution. The real-time technology method is rapid and accurate for FY genotyping. From now, we are able to detect the FY*X allele in all the alleles combinations studied. Regarding its significant frequency, the detection of the FY*X allele is useful for the correct typing of blood donors and recipients considering the therapeutic use of blood units and the preparation of test red blood cells for antibody screening.

European validation of a real-time PCR-based method for detection of Listeria monocytogenes in soft cheese.

PubMed

Gianfranceschi, Monica Virginia; Rodriguez-Lazaro, David; Hernandez, Marta; González-García, Patricia; Comin, Damiano; Gattuso, Antonietta; Delibato, Elisabetta; Sonnessa, Michele; Pasquali, Frederique; Prencipe, Vincenza; Sreter-Lancz, Zuzsanna; Saiz-Abajo, María-José; Pérez-De-Juan, Javier; Butrón, Javier; Kozačinski, Lidija; Tomic, Danijela Horvatek; Zdolec, Nevijo; Johannessen, Gro S; Jakočiūnė, Džiuginta; Olsen, John Elmerdahl; De Santis, Paola; Lovari, Sarah; Bertasi, Barbara; Pavoni, Enrico; Paiusco, Antonella; De Cesare, Alessandra; Manfreda, Gerardo; De Medici, Dario

2014-08-01

The classical microbiological method for detection of Listeria monocytogenes requires around 7 days for final confirmation, and due to perishable nature of RTE food products, there is a clear need for an alternative methodology for detection of this pathogen. This study presents an international (at European level) ISO 16140-based validation trial of a non-proprietary real-time PCR-based methodology that can generate final results in the following day of the analysis. This methodology is based on an ISO compatible enrichment coupled to a bacterial DNA extraction and a consolidated real-time PCR assay. Twelve laboratories from six European countries participated in this trial, and soft cheese was selected as food model since it can represent a difficult matrix for the bacterial DNA extraction and real-time PCR amplification. The limit of detection observed was down to 10 CFU per 25 of sample, showing excellent concordance and accordance values between samples and laboratories (>75%). In addition, excellent values were obtained for relative accuracy, specificity and sensitivity (82.75%, 96.70% and 97.62%, respectively) when the results obtained for the real-time PCR-based methods were compared to those of the ISO 11290-1 standard method. An interesting observation was that the L. monocytogenes detection by the real-time PCR method was less affected in the presence of Listeria innocua in the contaminated samples, proving therefore to be more reliable than the reference method. The results of this international trial demonstrate that the evaluated real-time PCR-based method represents an excellent alterative to the ISO standard since it shows a higher performance as well as reduce the extent of the analytical process, and can be easily implemented routinely by the competent authorities and food industry laboratories. Copyright © 2014 Elsevier B.V. All rights reserved.

Assessment of Liver Fibrosis Using Real-time Shear-wave Elastography for Patients with Hepatitis B e Antigen-negative Chronic Hepatitis B and Alanine Transaminase <2 Times the Upper Limit of Normal.

PubMed

Liu, Jing-Hua; Zou, Yu; Chang, Wei; Wu, Jun; Zou, Yu; Xie, Yu-Chen; Lu, Yong-Ping; Wei, Jia

2017-01-01

We assessed liver fibrosis using real-time shear-wave elastography (SWE) combined with liver biopsy (LB) for patients with hepatitis B e antigen (HBeAg)-negative chronic hepatitis B (CHB) and alanine transaminase < 2 times the upper limit of normal and hepatitis B virus DNA < 2000 IU/ml. A total of 107 patients met the inclusion criteria. Real- ime SWE and ultrasoundassisted liver biopsies were consecutively performed. Fibrosis was staged according to the METAVIR scoring system. Analyses of receiver operating characteristic curve were performed to calculate the optimal area under the receiver operating characteristic curve for F0-F1 versus F2-F4, F0-F2 versus F3-F4, and F0-F3 versus F4 for real-time SWE. The most concurrent liver fibrosis degrees were between F1 and F2 for these HBeAg-negative CHB patients. Liver stiffness increased in parallel with the degree of liver fibrosis using SWE measurements. The area under the receiver operating characteristic curves was 0.881 (95% confidence interval [CI]: 0.704-1.000) for SWE (p = 0.004); 0.912 (95% CI: 0.836-0.987) for SWE (p = 0.000); 0.981 (95% CI: 0.956-1.000) for SWE (p = 0.000); 0.974 (95% CI: 0.936-1.000) for SWE (p = 0.000) when comparing F0 versus F1-F4, F0-F1 versus F2-F4, F0-F2 versus F3-F4, and F0-F3 versus F4, respectively. SWE has the advantage of providing an image of liver stiffness in real-time. As an alternative to LB, the development of all these noninvasive methods for dynamic evaluation of liver fibrosis will decrease the need for LB, making clinical care safer and more convenient for patients with liver diseases.

The Case For Prediction-based Best-effort Real-time Systems.

DTIC Science & Technology

1999-01-01

Real - time Systems Peter A. Dinda Loukas Kallivokas January...DISTRIBUTION STATEMENT A Approved for Public Release Distribution Unlimited DTIG QUALBR DISSECTED X The Case For Prediction-based Best-effort Real - time Systems Peter...Mellon University Pittsburgh, PA 15213 A version of this paper appeared in the Seventh Workshop on Parallel and Distributed Real - Time Systems

Securing Real-Time Sessions in an IMS-Based Architecture

NASA Astrophysics Data System (ADS)

Cennamo, Paolo; Fresa, Antonio; Longo, Maurizio; Postiglione, Fabio; Robustelli, Anton Luca; Toro, Francesco

The emerging all-IP mobile network infrastructures based on 3rd Generation IP Multimedia Subsystem philosophy are characterised by radio access technology independence and ubiquitous connectivity for mobile users. Currently, great focus is being devoted to security issues since most of the security threats presently affecting the public Internet domain, and the upcoming ones as well, are going to be suffered by mobile users in the years to come. While a great deal of research activity, together with standardisation efforts and experimentations, is carried out on mechanisms for signalling protection, very few integrated frameworks for real-time multimedia data protection have been proposed in a context of IP Multimedia Subsystem, and even fewer experimental results based on testbeds are available. In this paper, after a general overview of the security issues arising in an advanced IP Multimedia Subsystem scenario, a comprehensive infrastructure for real-time multimedia data protection, based on the adoption of the Secure Real-Time Protocol, is proposed; then, the development of a testbed incorporating such functionalities, including mechanisms for key management and cryptographic context transfer, and allowing the setup of Secure Real-Time Protocol sessions is presented; finally, experimental results are provided together with quantitative assessments and comparisons of system performances for audio sessions with and without the adoption of the Secure Real-Time Protocol framework.

Elasticity-based three dimensional ultrasound real-time volume rendering

NASA Astrophysics Data System (ADS)

Boctor, Emad M.; Matinfar, Mohammad; Ahmad, Omar; Rivaz, Hassan; Choti, Michael; Taylor, Russell H.

2009-02-01

Volumetric ultrasound imaging has not gained wide recognition, despite the availability of real-time 3D ultrasound scanners and the anticipated potential of 3D ultrasound imaging in diagnostic and interventional radiology. Their use, however, has been hindered by the lack of real-time visualization methods that are capable of producing high quality 3D rendering of the target/surface of interest. Volume rendering is a known visualization method, which can display clear surfaces out of the acquired volumetric data, and has an increasing number of applications utilizing CT and MRI data. The key element of any volume rendering pipeline is the ability to classify the target/surface of interest by setting an appropriate opacity function. Practical and successful real-time 3D ultrasound volume rendering can be achieved in Obstetrics and Angio applications where setting these opacity functions can be done rapidly, and reliably. Unfortunately, 3D ultrasound volume rendering of soft tissues is a challenging task due to the presence of significant amount of noise and speckle. Recently, several research groups have shown the feasibility of producing 3D elasticity volume from two consecutive 3D ultrasound scans. This report describes a novel volume rendering pipeline utilizing elasticity information. The basic idea is to compute B-mode voxel opacity from the rapidly calculated strain values, which can also be mixed with conventional gradient based opacity function. We have implemented the volume renderer using GPU unit, which gives an update rate of 40 volume/sec.

Hypersonic Research Vehicle (HRV) real-time flight test support feasibility and requirements study. Part 1: Real-time flight experiment support

NASA Technical Reports Server (NTRS)

Rediess, Herman A.; Ramnath, Rudrapatna V.; Vrable, Daniel L.; Hirvo, David H.; Mcmillen, Lowell D.; Osofsky, Irving B.

1991-01-01

The results are presented of a study to identify potential real time remote computational applications to support monitoring HRV flight test experiments along with definitions of preliminary requirements. A major expansion of the support capability available at Ames-Dryden was considered. The focus is on the use of extensive computation and data bases together with real time flight data to generate and present high level information to those monitoring the flight. Six examples were considered: (1) boundary layer transition location; (2) shock wave position estimation; (3) performance estimation; (4) surface temperature estimation; (5) critical structural stress estimation; and (6) stability estimation.

High-speed railway real-time localization auxiliary method based on deep neural network

NASA Astrophysics Data System (ADS)

Chen, Dongjie; Zhang, Wensheng; Yang, Yang

2017-11-01

High-speed railway intelligent monitoring and management system is composed of schedule integration, geographic information, location services, and data mining technology for integration of time and space data. Assistant localization is a significant submodule of the intelligent monitoring system. In practical application, the general access is to capture the image sequences of the components by using a high-definition camera, digital image processing technique and target detection, tracking and even behavior analysis method. In this paper, we present an end-to-end character recognition method based on a deep CNN network called YOLO-toc for high-speed railway pillar plate number. Different from other deep CNNs, YOLO-toc is an end-to-end multi-target detection framework, furthermore, it exhibits a state-of-art performance on real-time detection with a nearly 50fps achieved on GPU (GTX960). Finally, we realize a real-time but high-accuracy pillar plate number recognition system and integrate natural scene OCR into a dedicated classification YOLO-toc model.

Real-time flutter boundary prediction based on time series models

NASA Astrophysics Data System (ADS)

Gu, Wenjing; Zhou, Li

2018-03-01

For the purpose of predicting the flutter boundary in real time during flutter flight tests, two time series models accompanied with corresponding stability criterion are adopted in this paper. The first method simplifies a long nonstationary response signal as many contiguous intervals and each is considered to be stationary. The traditional AR model is then established to represent each interval of signal sequence. While the second employs a time-varying AR model to characterize actual measured signals in flutter test with progression variable speed (FTPVS). To predict the flutter boundary, stability parameters are formulated by the identified AR coefficients combined with Jury's stability criterion. The behavior of the parameters is examined using both simulated and wind-tunnel experiment data. The results demonstrate that both methods show significant effectiveness in predicting the flutter boundary at lower speed level. A comparison between the two methods is also given in this paper.

Real-Time PCR-Based Quantitation Method for the Genetically Modified Soybean Line GTS 40-3-2.

PubMed

Kitta, Kazumi; Takabatake, Reona; Mano, Junichi

2016-01-01

This chapter describes a real-time PCR-based method for quantitation of the relative amount of genetically modified (GM) soybean line GTS 40-3-2 [Roundup Ready(®) soybean (RRS)] contained in a batch. The method targets a taxon-specific soybean gene (lectin gene, Le1) and the specific DNA construct junction region between the Petunia hybrida chloroplast transit peptide sequence and the Agrobacterium 5-enolpyruvylshikimate-3-phosphate synthase gene (epsps) sequence present in GTS 40-3-2. The method employs plasmid pMulSL2 as a reference material in order to quantify the relative amount of GTS 40-3-2 in soybean samples using a conversion factor (Cf) equal to the ratio of the RRS-specific DNA to the taxon-specific DNA in representative genuine GTS 40-3-2 seeds.

Legionella confirmation in cooling tower water. Comparison of culture, real-time PCR and next generation sequencing.

PubMed

Farhat, Maha; Shaheed, Raja A; Al-Ali, Haider H; Al-Ghamdi, Abdullah S; Al-Hamaqi, Ghadeer M; Maan, Hawraa S; Al-Mahfoodh, Zainab A; Al-Seba, Hussain Z

2018-02-01

To investigate the presence of Legionella spp in cooling tower water. Legionella proliferation in cooling tower water has serious public health implications as it can be transmitted to humans via aerosols and cause Legionnaires' disease. Samples of cooling tower water were collected from King Fahd Hospital of the University (KFHU) (Imam Abdulrahman Bin Faisal University, 2015/2016). The water samples were analyzed by a standard Legionella culture method, real-time polymerase chain reaction (RT-PCR), and 16S rRNA next-generation sequencing. In addition, the bacterial community composition was evaluated. All samples were negative by conventional Legionella culture. In contrast, all water samples yielded positive results by real-time PCR (105 to 106 GU/L). The results of 16S rRNA next generation sequencing showed high similarity and reproducibility among the water samples. The majority of sequences were Alpha-, Beta-, and Gamma-proteobacteria, and Legionella was the predominant genus. The hydrogen-oxidizing gram-negative bacterium Hydrogenophaga was present at high abundance, indicating high metabolic activity. Sphingopyxis, which is known for its resistance to antimicrobials and as a pioneer in biofilm formation, was also detected. Our findings indicate that monitoring of Legionella in cooling tower water would be enhanced by use of both conventional culturing and molecular methods.

Identification of phlebotomine sand fly blood meals by real-time PCR.

PubMed

Sales, Kamila Gaudêncio da Silva; Costa, Pietra Lemos; de Morais, Rayana Carla Silva; Otranto, Domenico; Brandão-Filho, Sinval Pinto; Cavalcanti, Milena de Paiva; Dantas-Torres, Filipe

2015-04-16

Phlebotomine sand flies are blood-feeding insects of great medical and veterinary significance acting as vectors of Leishmania parasites. Studying the blood-feeding pattern of these insects may help in the understanding of their interactions with potential reservoir hosts of Leishmania parasites. In this study, we developed real time PCR assays for the identification of sand fly blood meal. Six pairs of primers were designed based on cytochrome b gene sequences available in GenBank of the following potential hosts: dog, cat, horse, chicken, black rat, and human. Firstly, SYBR Green-based real time PCR assays were conducted using a standard curve with eight different concentrations (i.e., 10 ng, 1 ng, 100 pg, 10 pg, 1 pg, 100 fg, 10 fg and 1 fg per 2 μl) of DNA samples extracted from EDTA blood samples from each target animal. Then, DNA samples extracted from field-collected engorged female sand flies belonging to three species (i.e., Lutzomyia longipalpis, L. migonei and L. lenti) were tested by the protocols standardized herein. Additionally, female sand flies were experimentally fed on a black rat (Rattus rattus) and used for evaluating the time course of the detection of the protocol targeting this species. The protocols performed well with detection limits of 10 pg to 100 fg. Field-collected female sand flies were fed on blood from humans (73%), chickens (23%), dogs (22%), horses (15%), black rats (11%) and cats (2%). Interestingly, 76.1% of the L. longipalpis females were positive for human blood. In total, 48% of the tested females were fed on single sources, 31% on two and 12% on three. The analysis of the time course showed that the real time PCR protocol targeting the black rat DNA was able to detect small amounts of the host DNA up to 5 days after the blood meal. The real time PCR assays standardized herein successfully detected small amounts of host DNA in female sand flies fed on different vertebrate species and, specifically for the black

Real-time microfluidic recombinase polymerase amplification for the toxin B gene of Clostridium difficile on a SlipChip platform.

PubMed

Tsaloglou, M-N; Watson, R J; Rushworth, C M; Zhao, Y; Niu, X; Sutton, J M; Morgan, H

2015-01-07

Clostridium difficile is one of the key bacterial pathogens that cause infectious diarrhoea both in the developed and developing world. Isothermal nucleic acid amplification methods are increasingly used for identification of toxinogenic infection by clinical labs. For this purpose, we developed a low-cost microfluidic platform based on the SlipChip concept and implemented real-time isothermal recombinase polymerase amplification (RPA). The on-chip RPA assay targets the Clostridium difficile toxin B gene (tcdB) coding for toxin B, one of the proteins responsible for bacterial toxicity. The device was fabricated in clear acrylic using rapid prototyping methods. It has six replicate 500 nL reaction wells as well as two sets of 500 nL control wells. The reaction can be monitored in real-time using exonuclease fluorescent probes with an initial sample volume of as little as 6.4 μL. We demonstrated a limit of detection of 1000 DNA copies, corresponding to 1 fg, at a time-to-result of <20 minutes. This miniaturised platform for pathogen detection has potential for use in resource-limited environments or at the point-of-care because of its ease of use and low cost, particularly if combined with preserved reagents.

Real-time fluorescence target/background (T/B) ratio calculation in multimodal endoscopy for detecting GI tract cancer

NASA Astrophysics Data System (ADS)

Jiang, Yang; Gong, Yuanzheng; Wang, Thomas D.; Seibel, Eric J.

2017-02-01

Multimodal endoscopy, with fluorescence-labeled probes binding to overexpressed molecular targets, is a promising technology to visualize early-stage cancer. T/B ratio is the quantitative analysis used to correlate fluorescence regions to cancer. Currently, T/B ratio calculation is post-processing and does not provide real-time feedback to the endoscopist. To achieve real-time computer assisted diagnosis (CAD), we establish image processing protocols for calculating T/B ratio and locating high-risk fluorescence regions for guiding biopsy and therapy in Barrett's esophagus (BE) patients. Methods: Chan-Vese algorithm, an active contour model, is used to segment high-risk regions in fluorescence videos. A semi-implicit gradient descent method was applied to minimize the energy function of this algorithm and evolve the segmentation. The surrounding background was then identified using morphology operation. The average T/B ratio was computed and regions of interest were highlighted based on user-selected thresholding. Evaluation was conducted on 50 fluorescence videos acquired from clinical video recordings using a custom multimodal endoscope. Results: With a processing speed of 2 fps on a laptop computer, we obtained accurate segmentation of high-risk regions examined by experts. For each case, the clinical user could optimize target boundary by changing the penalty on area inside the contour. Conclusion: Automatic and real-time procedure of calculating T/B ratio and identifying high-risk regions of early esophageal cancer was developed. Future work will increase processing speed to <5 fps, refine the clinical interface, and apply to additional GI cancers and fluorescence peptides.

Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications.

PubMed

Lassiter, S J; Stryjewski, W; Legendre, B L; Erdmann, R; Wahl, M; Wurm, J; Peterson, R; Middendorf, L; Soper, S A

2000-11-01

A compact time-resolved near-IR fluorescence imager was constructed to obtain lifetime and intensity images of DNA sequencing slab gels. The scanner consisted of a microscope body with f/1.2 relay optics onto which was mounted a pulsed diode laser (repetition rate 80 MHz, lasing wavelength 680 nm, average power 5 mW), filtering optics, and a large photoactive area (diameter 500 microns) single-photon avalanche diode that was actively quenched to provide a large dynamic operating range. The time-resolved data were processed using electronics configured in a conventional time-correlated single-photon-counting format with all of the counting hardware situated on a PC card resident on the computer bus. The microscope head produced a timing response of 450 ps (fwhm) in a scanning mode, allowing the measurement of subnano-second lifetimes. The time-resolved microscope head was placed in an automated DNA sequencer and translated across a 21-cm-wide gel plate in approximately 6 s (scan rate 3.5 cm/s) with an accumulation time per pixel of 10 ms. The sampling frequency was 0.17 Hz (duty cycle 0.0017), sufficient to prevent signal aliasing during the electrophoresis separation. Software (written in Visual Basic) allowed acquisition of both the intensity image and lifetime analysis of DNA bands migrating through the gel in real time. Using a dual-labeling (IRD700 and Cy5.5 labeling dyes)/two-lane sequencing strategy, we successfully read 670 bases of a control M13mp18 ssDNA template using lifetime identification. Comparison of the reconstructed sequence with the known sequence of the phage indicated the number of miscalls was only 2, producing an error rate of approximately 0.3% (identification accuracy 99.7%). The lifetimes were calculated using maximum likelihood estimators and allowed on-line determinations with high precision, even when short integration times were used to construct the decay profiles. Comparison of the lifetime base calling to a single

Comparison of Directigen Flu A+B with Real Time PCR in the Diagnosis of Influenza.

PubMed

Bosevska, Golubinka; Panovski, Nikola; Janceska, Elizabeta; Mikik, Vladimir; Topuzovska, Irena Kondova; Milenkovik, Zvonko

2015-01-01

Early diagnosis and treatment of patients with influenza is the reason why physicians need rapid high-sensitivity influenza diagnostic tests that require no complex lab equipment and can be performed and interpreted within 15 min. The Aim of this study was to compare the rapid Directigen Flu A+B test with real time PCR for detection of influenza viruses in the Republic of Macedonia. One-hundred-eight respiratory samples (combined nose and throat swabs) were routinely collected for detection of influenza virus during influenza seasons. Forty-one patients were pediatric cases and 59 were adult. Their mean age was 23 years. The patients were allocated into 6 age groups: 0-4 yrs, 5-9 yrs, 10-14 yrs, 15-19 yrs, 20-64 yrs and > 65 yrs. Each sample was tested with Directigen Flu A+B and CDC real time PCR kit for detection and typisation/subtypisation of influenza according to the lab diagnostic protocol. Directigen Flu A+B identified influenza A virus in 20 (18.5%) samples and influenza B virus in two 2 (1.9%) samples. The high specificity (100%) and PPV of Directigen Flu A+B we found in our study shows that the positive results do not need to be confirmed. The overall sensitivity of Directigen Flu A+B is 35.1% for influenza A virus and 33.0% for influenza B virus. The sensitivity for influenza A is higher among children hospitalized (45.0%) and outpatients (40.0%) versus adults. Directigen Flu A+B has relatively low sensitivity for detection of influenza viruses in combined nose and throat swabs. Negative results must be confirmed.

Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation.

PubMed

Jackson, Brendan R; Tarr, Cheryl; Strain, Errol; Jackson, Kelly A; Conrad, Amanda; Carleton, Heather; Katz, Lee S; Stroika, Steven; Gould, L Hannah; Mody, Rajal K; Silk, Benjamin J; Beal, Jennifer; Chen, Yi; Timme, Ruth; Doyle, Matthew; Fields, Angela; Wise, Matthew; Tillman, Glenn; Defibaugh-Chavez, Stephanie; Kucerova, Zuzana; Sabol, Ashley; Roache, Katie; Trees, Eija; Simmons, Mustafa; Wasilenko, Jamie; Kubota, Kristy; Pouseele, Hannes; Klimke, William; Besser, John; Brown, Eric; Allard, Marc; Gerner-Smidt, Peter

2016-08-01

Listeria monocytogenes (Lm) causes severe foodborne illness (listeriosis). Previous molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE), were critical in detecting outbreaks that led to food safety improvements and declining incidence, but PFGE provides limited genetic resolution. A multiagency collaboration began performing real-time, whole-genome sequencing (WGS) on all US Lm isolates from patients, food, and the environment in September 2013, posting sequencing data into a public repository. Compared with the year before the project began, WGS, combined with epidemiologic and product trace-back data, detected more listeriosis clusters and solved more outbreaks (2 outbreaks in pre-WGS year, 5 in WGS year 1, and 9 in year 2). Whole-genome multilocus sequence typing and single nucleotide polymorphism analyses provided equivalent phylogenetic relationships relevant to investigations; results were most useful when interpreted in context of epidemiological data. WGS has transformed listeriosis outbreak surveillance and is being implemented for other foodborne pathogens. Published by Oxford University Press for the Infectious Diseases Society of America 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Sequence Analysis of IncA/C and IncI1 Plasmids Isolated from Multidrug-Resistant Salmonella Newport Using Single-Molecule Real-Time Sequencing.

PubMed

Cao, Guojie; Allard, Marc; Hoffmann, Maria; Muruvanda, Tim; Luo, Yan; Payne, Justin; Meng, Kevin; Zhao, Shaohua; McDermott, Patrick; Brown, Eric; Meng, Jianghong

2018-06-01

Multidrug-resistant (MDR) plasmids play an important role in disseminating antimicrobial resistance genes. To elucidate the antimicrobial resistance gene compositions in A/C incompatibility complex (IncA/C) plasmids carried by animal-derived MDR Salmonella Newport, and to investigate the spread mechanism of IncA/C plasmids, this study characterizes the complete nucleotide sequences of IncA/C plasmids by comparative analysis. Complete nucleotide sequencing of plasmids and chromosomes of six MDR Salmonella Newport strains was performed using PacBio RSII. Open reading frames were assigned using prokaryotic genome annotation pipeline (PGAP). To understand genomic diversity and evolutionary relationships among Salmonella Newport IncA/C plasmids, we included three complete IncA/C plasmid sequences with similar backbones from Salmonella Newport and Escherichia coli: pSN254, pAM04528, and peH4H, and additional 200 draft chromosomes. With the exception of canine isolate CVM22462, which contained an additional IncI1 plasmid, each of the six MDR Salmonella Newport strains contained only the IncA/C plasmid. These IncA/C plasmids (including references) ranged in size from 80.1 (pCVM21538) to 176.5 kb (pSN254) and carried various resistance genes. Resistance genes floR, tetA, tetR, strA, strB, sul, and mer were identified in all IncA/C plasmids. Additionally, bla CMY-2 and sugE were present in all IncA/C plasmids, excepting pCVM21538. Plasmid pCVM22462 was capable of being transferred by conjugation. The IncI1 plasmid pCVM22462b in CVM22462 carried bla CMY-2 and sugE. Our data showed that MDR Salmonella Newport strains carrying similar IncA/C plasmids clustered together in the phylogenetic tree using chromosome sequences and the IncA/C plasmids from animal-derived Salmonella Newport contained diverse resistance genes. In the current study, we analyzed genomic diversities and phylogenetic relationships among MDR Salmonella Newport using complete plasmids and chromosome

Method for Real-Time Model Based Structural Anomaly Detection

NASA Technical Reports Server (NTRS)

Urnes, James M., Sr. (Inventor); Smith, Timothy A. (Inventor); Reichenbach, Eric Y. (Inventor)

2015-01-01

A system and methods for real-time model based vehicle structural anomaly detection are disclosed. A real-time measurement corresponding to a location on a vehicle structure during an operation of the vehicle is received, and the real-time measurement is compared to expected operation data for the location to provide a modeling error signal. A statistical significance of the modeling error signal to provide an error significance is calculated, and a persistence of the error significance is determined. A structural anomaly is indicated, if the persistence exceeds a persistence threshold value.

Real-time PCR detection and quantification of nine potential sources of fecal contamination by analysis of mitochondrial Cytochrome b targets

USGS Publications Warehouse

Schill, W.B.; Mathes, M.V.

2008-01-01

We designed and tested real-time PCR probe/primer sets to detect and quantify Cytochrome b sequences of mitochondrial DNA (mtDNA) from nine vertebrate species of pet (dog), farm (cow, chicken, sheep, horse, pig), wildlife (Canada goose, white-tailed deer), and human. Linear ranges of the assays were from 101 to 108 copies/??l. To formally test the performance of the assays, twenty blinded fecal suspension samples were analyzed by real-time PCR to identify the source of the feces. Sixteen of the twenty samples were correctly and unambiguously identified. Average sensitivity was calculated to be 0.850, while average specificity was found to be 0.994. One beef cow sample was not detected, but mtDNA from 11 other beef cattle of both sexes and varying physiological states was found in concentrations similar (3.45 ?? 107 copies/g) to thatfound in human feces (1.1 ?? 107 copies/g). Thus, environmental conditions and sample handling are probably important factors for successful detection of fecal mtDNA. When sewage samples were analyzed, only human mtDNA (7.2 ?? 104 copies/100 mL) was detected. With a detection threshold of 250 copies/reaction, an efficient concentration and purification method resulted in a final detection limit for human feces of 1.8 mg/100 mL water.

A Miniature Forward-imaging B-scan Optical Coherence Tomography Probe to Guide Real-time Laser Ablation

PubMed Central

Li, Zhuoyan; Shen, Jin H.; Kozub, John A.; Prasad, Ratna; Lu, Pengcheng; Joos, Karen M.

2014-01-01

Background and Objective Investigations have shown that pulsed lasers tuned to 6.1 μm in wavelength are capable of ablating ocular and neural tissue with minimal collateral damage. This study investigated whether a miniature B-scan forward-imaging optical coherence tomography (OCT) probe can be combined with the laser to provide real-time visual feedback during laser incisions. Study Design/Methods and Materials A miniature 25-gauge B-scan forward-imaging OCT probe was developed and combined with a 250 μm hollow-glass waveguide to permit delivery of 6.1 μm laser energy. A gelatin mixture and both porcine corneal and retinal tissues were simultaneously imaged and lased (6.1 μm, 10 Hz, 0.4-0.7 mJ) through air. The ablation studies were observed and recorded in real time. The crater dimensions were measured using OCT imaging software (Bioptigen, Durham, NC). Histological analysis was performed on the ocular tissues. Results The combined miniature forward-imaging OCT and mid-infrared laser-delivery probe successfully imaged real-time tissue ablation in gelatin, corneal tissue, and retinal tissue. Application of a constant number of 60 pulses at 0.5 mJ/pulse to the gelatin resulted in a mean crater depth of 123 ± 15 μm. For the corneal tissue, there was a significant correlation between the number of pulses used and depth of the lased hole (Pearson correlation coefficient = 0.82; P = 0.0002). Histological analysis of the cornea and retina tissues showed discrete holes with minimal thermal damage. Conclusions A combined miniature OCT and laser -delivery probe can monitor real-time tissue laser ablation. With additional testing and improvements, this novel instrument has the future possibility of effectively guiding surgeries by simultaneously imaging and ablating tissue. PMID:24648326

Real-time feedback control of twin-screw wet granulation based on image analysis.

PubMed

Madarász, Lajos; Nagy, Zsombor Kristóf; Hoffer, István; Szabó, Barnabás; Csontos, István; Pataki, Hajnalka; Démuth, Balázs; Szabó, Bence; Csorba, Kristóf; Marosi, György

2018-06-04

The present paper reports the first dynamic image analysis-based feedback control of continuous twin-screw wet granulation process. Granulation of the blend of lactose and starch was selected as a model process. The size and size distribution of the obtained particles were successfully monitored by a process camera coupled with an image analysis software developed by the authors. The validation of the developed system showed that the particle size analysis tool can determine the size of the granules with an error of less than 5 µm. The next step was to implement real-time feedback control of the process by controlling the liquid feeding rate of the pump through a PC, based on the real-time determined particle size results. After the establishment of the feedback control, the system could correct different real-life disturbances, creating a Process Analytically Controlled Technology (PACT), which guarantees the real-time monitoring and controlling of the quality of the granules. In the event of changes or bad tendencies in the particle size, the system can automatically compensate the effect of disturbances, ensuring proper product quality. This kind of quality assurance approach is especially important in the case of continuous pharmaceutical technologies. Copyright © 2018 Elsevier B.V. All rights reserved.

Insecticidal components from field pea extracts: sequences of some variants of pea albumin 1b.

PubMed

Taylor, Wesley G; Sutherland, Daniel H; Olson, Douglas J H; Ross, Andrew R S; Fields, Paul G

2004-12-15

Methanol soluble insecticidal peptides with masses of 3752, 3757, and 3805 Da, isolated from crude extracts (C8 extracts) derived from the protein-enriched flour of commercial field peas [Pisum sativum (L.)], were purified by reversed phase chromatography and, after reduction and alkylation, were sequenced by matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry with the aid of various peptidases. These major peptides were variants of pea albumin 1b (PA1b) with methionine sulfoxide rather than methionine at position 12. Peptide 3752 showed additional variations at positions 29 (valine for isoleucine) and 34 (histidine for asparagine). A minor, 37 amino acid peptide with a molecular mass of 3788 Da was also sequenced and differed from a known PA1b variant at positions 1, 25, and 31. Sequence variants of PA1b with their molecular masses were compiled, and variants that matched the accurate masses of the experimental peptides were used to narrow the search. MALDI postsource decay experiments on pronase fragments helped to confirm the sequences. Whole and dehulled field peas gave insecticidal C8 extracts in the laboratory that were enriched in peptides with masses of 3736, 3741, and 3789 Da, as determined by high-performance liquid chromatography (HPLC) and electrospray ionization mass spectrometry. It was therefore concluded that oxidation of the methionine residues to methionine sulfoxide occurred primarily during the processing of dehulled peas in a mill.

All-digital 1.2-Gbit/s real-time HDTV VTR

NASA Astrophysics Data System (ADS)

Thorpe, Laurence J.; Yoshinaka, T.

1992-08-01

In 1984 the first real-time HDTV video tape recorder was introduced. The HDV-1000 was an analog VTR using one inch metal oxide tape and standard SMPTE open reels. It utilized basic Type-C recording principles although also incorporating a considerably higher FM carrier frequency, twice the deviation, and slightly more preemphasis, - all to achieve a 10 MHz baseband video recording bandwidth capability. Four such component analog recording channels were utilized in parallel to achieve a total recording capability of 40 MHz - made up of 20 MHz for the green video signal (or Luminance Y) and 10 MHz each for the red and blue signals (or R-Y and B-Y components in the case of Y, R-Y, B-Y recording). Almost 150 of these machines supported the early pioneering years of HDTV development - worldwide - over the period 1984 to the late 1980's. The HDTV video signal format to which this VTR was designed was based upon the preliminary 1 125/60/16:9/2: 1 system - having specified system bandwiths of 20 MHz for Luminance Y, and 7.0MHz R-Y, and 5.5 MHz B-Y. The HDV-1000 proved to be a remarkably robust, reliable HD VTR workhorse and it early and firmly established the viability of reliable RD real-time image capture. Nevertheless, it's technical shortcomings were soon exposed by a creative and demanding international program production community. The limitations of two channels of analog audio recording, and about four generations of liD video recording in post-production were inconsistent with the needs of high-end program production. The 45 db signal to noise limitation also imposed a boundary to the quality of the HDTV tape to 35 mm film transfers being made by both Electron Beam and Laser Recording techniques. The HDV-1000 had, however, pushed the state of the art in analog FM recording to the boundary. Head and tape technologies were not expected to advance sufficiently to warrant a new generation in analog recording design. Attention thus turned to digital recording

Real-time tracking of tumor motions and deformations along the leaf travel direction with the aid of a synchronized dynamic MLC leaf sequencer.

PubMed

Tacke, Martin; Nill, Simeon; Oelfke, Uwe

2007-11-21

Advanced radiotherapeutical techniques like intensity-modulated radiation therapy (IMRT) are based on an accurate knowledge of the location of the radiation target. An accurate dose delivery, therefore, requires a method to account for the inter- and intrafractional target motion and the target deformation occurring during the course of treatment. A method to compensate in real time for changes in the position and shape of the target is the use of a dynamic multileaf collimator (MLC) technique which can be devised to automatically arrange the treatment field according to real-time image information. So far, various approaches proposed for leaf sequencers have had to rely on a priori known target motion data and have aimed to optimize the overall treatment time. Since for a real-time dose delivery the target motion is not known a priori, the velocity range of the leading leaves is restricted by a safety margin to c x v(max) while the following leaves can travel with an additional maximum speed to compensate for the respective target movements. Another aspect to be considered is the tongue and groove effect. A uniform radiation field can only be achieved if the leaf movements are synchronized. The method presented in this note is the first to combine a synchronizing sequencer and real-time tracking with a dynamic MLC. The newly developed algorithm is capable of online optimizing the leaf velocities by minimizing the overall treatment time while at the same time it synchronizes the leaf trajectories in order to avoid the tongue and groove effect. The simultaneous synchronization is performed with the help of an online-calculated mid-time leaf trajectory which is common for all leaf pairs and which takes into account the real-time target motion and deformation information.

Real-Time Sequence-Validated Loop-Mediated Isothermal Amplification Assays for Detection of Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

PubMed Central

Bhadra, Sanchita; Jiang, Yu Sherry; Kumar, Mia R.; Johnson, Reed F.; Hensley, Lisa E.; Ellington, Andrew D.

2015-01-01

The Middle East respiratory syndrome coronavirus (MERS-CoV), an emerging human coronavirus, causes severe acute respiratory illness with a 35% mortality rate. In light of the recent surge in reported infections we have developed asymmetric five-primer reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for detection of MERS-CoV. Isothermal amplification assays will facilitate the development of portable point-of-care diagnostics that are crucial for management of emerging infections. The RT-LAMP assays are designed to amplify MERS-CoV genomic loci located within the open reading frame (ORF)1a and ORF1b genes and upstream of the E gene. Additionally we applied one-step strand displacement probes (OSD) for real-time sequence-specific verification of LAMP amplicons. Asymmetric amplification effected by incorporating a single loop primer in each assay accelerated the time-to-result of the OSD-RT-LAMP assays. The resulting assays could detect 0.02 to 0.2 plaque forming units (PFU) (5 to 50 PFU/ml) of MERS-CoV in infected cell culture supernatants within 30 to 50 min and did not cross-react with common human respiratory pathogens. PMID:25856093

A small test of a sequence-based typing method: definition of the B*1520 allele.

PubMed

Domena, J D; Little, A M; Arnett, K L; Adams, E J; Marsh, S G; Parham, P

1994-10-01

Santamaria et al. (Human Immunology 1993 37: 39-50) describe a method of sequence-based typing (SBT) for HLA-A, B and C alleles said to give "unambiguous typing of any sample, heterozygous or homozygous, without requiring additional typing information". From SBT analysis, which involves determination of partial sequences of mixed alleles, these investigators reported that cell lines KT17 (HLA-B35,62) and OLGA (HLA-B62) from the reference panel of the 10th International Histocompatibility Workshop express novel variants of HLA-B15 (B1501-MN6) and HLA-B35 (B3501-MN7) respectively. To study further the novel alleles, we cloned and sequenced full-length HLA-B cDNA clones isolated from the KT17 and OLGA cell lines. We find that KT17 expresses B*3501, as assigned by SBT, and B*1501, the common allele encoding the B62 antigen. We were unable to confirm that KT17 expresses the novel B1501-MN6 variant identified by SBT. For OLGA our analysis confirms the partial sequences obtained by SBT. Thus OLGA expresses B*1501 and a novel HLA-B allele. The complete sequence of the latter shows it is a hybrid having exons 1 and 2 in common with B*1501 and other B15 subtypes and exons 3-7 in common with B*3501 and related molecules including B*5301 and B*5801. The novel allele has been designated B*1520 because of its sequence similarity with the B15 group; furthermore, serological analysis shows that the B*1520 product does not express epitopes in common with either B35, B53 or B58. The B*1520 heavy chain has a similar isoelectric point to A*3101; B*1520 was undetected by previous applications of isoelectric focusing because B*1520 and A31 are both expressed by OLGA. In conclusion, HLA-B typing of two cell lines by cDNA cloning and sequencing gives concordant results with SBT for three of the four alleles. The cause of the discrepancy for the fourth allele is unknown, however, this finding indicates that the novel HLA-A, B and C sequences emerging from SBT studies need independent

Identification of four novel HLA-B alleles, B*1590, B*1591, B*2726, and B*4705, from an East African population by high-resolution sequence-based typing.

PubMed

Luo, M; Mao, X; Plummer, F A

2005-02-01

We report here four novel HLA-B alleles, B*1590, B*1591, B*2726, and B*4705, identified from an East African population during sequence-based HLA-B typing. The novel alleles were confirmed by sequencing two separate polymerase chain reaction products, and by molecular cloning and sequencing multiple clones. B*1590 is identical to B*1510 at exon 2 and exon 3, except for a difference (GCCGTC) at codon 158. Sequence differences at codon 152 (GAGGTG) and codon 167 (TGGTCG) differentiate B*1591 from B*1503 at exon 3. B*2726 is identical to B*2708 at exon 2 and exon 3, except for a difference (AAGCAG) at codon 70. B*4705 was identified in three Kenyan women. The allele is identical to B*47010101/02 at exon 2 and exon 3, except for differences at codon 97 (AGGAAT) and codon 99 (TTTTAT). These new alleles have been named by the WHO Nomenclature Committee. Identification of these novel HLA-B alleles reflects the genetic diversity of this East African population.

Comparative diagnostic evaluation of OMP31 gene based TaqMan® real-time PCR assay with visual LAMP assay and indirect ELISA for caprine brucellosis.

PubMed

Saini, Suman; Gupta, V K; Gururaj, K; Singh, D D; Pawaiya, R V S; Gangwar, N K; Mishra, A K; Dwivedi, Deepak; Andani, Dimple; Kumar, Ashok; Goswami, T K

2017-08-01

Brucellosis is one of the leading causes of abortion in domestic animals that imposes costs on both economy and society. The disease is highly zoonotic and poses risk to animal handlers due to its zoonotic nature. It causes stillbirth, loss of kids and abortion in last term of pregnancy. Reproductive damage includes infertility in does and orchitis and epididymitis in breeding bucks, which result in high financial losses to farmers and the agriculture industry as a whole. It requires highly sensitive and specific assays to diagnose the disease at field level. In the current study, a visual loop-mediated isothermal amplification (LAMP) assay and the TaqMan® real-time PCR were developed with high sensitivity and specificity. For the TaqMan® probe, real-time PCR primers were developed using Omp31 gene as target and primers were designed using discontiguous conserved sequences of Omp31 gene. The Omp31 probes were designed by attaching 6-FAM reporter dye at the 5' end and BHQ-1 quencher at the 3' end. Published primers were used for visual LAMP assay targeting the Omp25 gene. Sensitivity of the standardized visual LAMP assay and TaqMan® real-time PCR assay was determined by serial dilution of positive Brucella melitensis DNA (10 2 to 10 -4  ng) obtained from standard culture. The TaqMan® probe real-time assay can detect as low as 100 fg of B. melitensis DNA, whereas culture from vaginal swab washings has a limit of detection (LOD) of only 1 cfu/ml. Similarly, the visual LAMP assay can detect as low as 10 fg of B. melitensis DNA as compared to an LOD of 30 cfu/ml from culture of vaginal swab washings. Both assays were compared with serological tests (serum tube agglutination test (STAT) and indirect enzyme-linked immunosorbent assay (iELISA)) for diagnostic sensitivity and specificity. Diagnostic sensitivities and specificities for TaqMan® real-time PCR vs. LAMP assays were 98 and 100% vs. 100 and 97.8%, respectively. Results of visual LAMP assay indicated that

Selection and validation of reference genes for quantitative real-time PCR in Artemisia sphaerocephala based on transcriptome sequence data.

PubMed

Hu, Xiaowei; Zhang, Lijing; Nan, Shuzhen; Miao, Xiumei; Yang, Pengfang; Duan, Guoqin; Fu, Hua

2018-05-30

Artemisia sphaerocephala, a dicotyledonous perennial semi-shrub belonging to the Artemisia genus of the Compositae family, is widely distributed in northwestern China. This shrub is one of the most important pioneer plants which is capable of protecting rangelands from wind erosion. It therefore plays a vital role in maintaining desert ecosystem stability. In addition, to its use as a forage grass, it has excellent prospective applications as a source of plant oil and as a plant-based fuel. The use of internal genes is the basis for accurately assessing Real time quantitative PCR. In this study, based on transcriptome data of A. sphaerocephala, we analyzed 21 candidate internal genes to determine the optimal internal genes in this shrub. The stabilities of candidate genes were evaluated in 16 samples of A. sphaerocephala. Finally, UBC9 and TIP41-like were determined as the optimal reference genes in A. sphaerocephala by Delta Ct and three various programs. There were GeNorm, NormFinder and BestKeeper. Copyright © 2018 Elsevier B.V. All rights reserved.

Complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1 using PacBio single-molecule real-time technology

USDA-ARS?s Scientific Manuscript database

We report the complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1 isolated in Minnesota, USA. The R1-1 genome, generated by de novo assembly of PacBio sequencing data, is the first complete genome sequence available for this subspecies....

Development of real-time PCR for detection and quantitation of Streptococcus parauberis.

PubMed

Nguyen, T L; Lim, Y J; Kim, D-H; Austin, B

2016-01-01

Streptococcus parauberis is an increasing threat to aquaculture of olive flounder, Paralichthys olivaceus Temminck & Schlegel, in South Korea. We developed a real-time polymerase chain reaction (PCR) method using the TaqMan probe assay to detect and quantify S. parauberis by targeting the gyrB gene sequences, which are effective for molecular analysis of the genus Streptococcus. Our real-time PCR assay is capable of detecting 10 fg of genomic DNA per reaction. The intra- and interassay coefficient of variation (CV) values ranged from 0.42-1.95%, demonstrating that the assay has good reproducibility. There was not any cross-reactivity to Streptococcus iniae or to other streptococcal/lactococcal fish pathogens, such as S. agalactiae and Lactococcus garvieae, indicating that the assay is highly specific to S. parauberis. The results of the real-time PCR assay corresponded well to those of conventional culture assays for S. parauberis from inoculated tissue homogenates (r = 0.957; P < 0.05). Hence, this sensitive and specific real-time PCR is a valuable tool for diagnostic quantitation of S. parauberis in clinical samples. © 2014 John Wiley & Sons Ltd.

Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR.

PubMed

Osimani, Andrea; Milanović, Vesna; Garofalo, Cristiana; Cardinali, Federica; Roncolini, Andrea; Sabbatini, Riccardo; De Filippis, Francesca; Ercolini, Danilo; Gabucci, Claudia; Petruzzelli, Annalisa; Tonucci, Franco; Clementi, Francesca; Aquilanti, Lucia

2018-07-02

The present study aimed to identify the microbiota present in six species of processed edible insects produced in Thailand and marketed worldwide via the internet, namely, giant water bugs (Belostoma lutarium), black ants (Polyrhachis), winged termites (alates, Termitoidae), rhino beetles (Hyboschema contractum), mole crickets (Gryllotalpidae), and silkworm pupae (Bombyx mori). For each species, two samples of boiled, dried and salted insects were purchased. The microbial DNA was extracted from the insect samples and subjected to polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), high-throughput sequencing and qualitative real-time PCR assays. The microbiota of the analyzed samples were widely characterized by the presence of spore-forming bacteria mainly represented by the genera Bacillus and Clostridium. Moreover, the genera Anaerobacillus, Paenibacillus, Geobacillus, Pseudomonas, Stenotrophomonas, Massilia, Delftia, Lactobacillus, Staphylococcus, Streptococcus, Vagococcus, and Vibrio were also detected. Real-time PCR allowed for ascertainment of the absence of Coxiella burnetii, Shiga toxin-producing E. coli (STEC), and Pseudomonas aeruginosa in all samples. The results of this study confirm the importance of combining different molecular techniques to characterize the biodiversity of complex ecosystems such as edible insects. The presence of potential human pathogens suggests the need for a careful application of good manufacturing practices during insect processing. This study provides further data that will be useful in risk analyses of edible insects as a novel food source. Copyright © 2018 Elsevier B.V. All rights reserved.

Real-time PCR detection chemistry.

PubMed

Navarro, E; Serrano-Heras, G; Castaño, M J; Solera, J

2015-01-15

Real-time PCR is the method of choice in many laboratories for diagnostic and food applications. This technology merges the polymerase chain reaction chemistry with the use of fluorescent reporter molecules in order to monitor the production of amplification products during each cycle of the PCR reaction. Thus, the combination of excellent sensitivity and specificity, reproducible data, low contamination risk and reduced hand-on time, which make it a post-PCR analysis unnecessary, has made real-time PCR technology an appealing alternative to conventional PCR. The present paper attempts to provide a rigorous overview of fluorescent-based methods for nucleic acid analysis in real-time PCR described in the literature so far. Herein, different real-time PCR chemistries have been classified into two main groups; the first group comprises double-stranded DNA intercalating molecules, such as SYBR Green I and EvaGreen, whereas the second includes fluorophore-labeled oligonucleotides. The latter, in turn, has been divided into three subgroups according to the type of fluorescent molecules used in the PCR reaction: (i) primer-probes (Scorpions, Amplifluor, LUX, Cyclicons, Angler); (ii) probes; hydrolysis (TaqMan, MGB-TaqMan, Snake assay) and hybridization (Hybprobe or FRET, Molecular Beacons, HyBeacon, MGB-Pleiades, MGB-Eclipse, ResonSense, Yin-Yang or displacing); and (iii) analogues of nucleic acids (PNA, LNA, ZNA, non-natural bases: Plexor primer, Tiny-Molecular Beacon). In addition, structures, mechanisms of action, advantages and applications of such real-time PCR probes and analogues are depicted in this review. Copyright © 2014 Elsevier B.V. All rights reserved.

[Clinical utility of real-time fluorescent PCR for combined detection of anaplastic lymphoma kinase and c-ros oncogene 1 receptor tyrosine kinase in non-small cell lung cancer].

PubMed

Bai, D Y; Zhang, H P; Zhong, S; Suo, W H; Gao, D H; Ding, Y; Tu, J H

2016-12-23

Objective: To investigate the clinical application value of combined detection of ALK fusion gene and c-ros oncogene 1 receptor tyrosine kinase (ROS1) fusion gene in non-small cell lung cancer (NSCLC) using real-time fluorescent PCR. Methods: A kit for combined detection of ALK fusion gene and ROS1 fusion gene based on fluorescent PCR was used to simultaneously detect the two fusion genes in 302 cases of NSCLC specimens. The results were validated through Sanger sequencing. The consistency of the two detection methods was analyzed. Results: All 302 cases of NSCLC specimens were successfully analyzed through fluorescent PCR (302/302). 12 cases (4.0%) were found to contain ALK fusion gene, including 3 cases with ALK-M1, 3 with ALK-M2, 3 with ALK-M3, 1 with ALK-M4, and 2 with ALK-M6 fusion gene.12 cases (4.0%) were found to contain ROS1 fusion gene, including 1 case with ROS1-M7, 8 cases with ROS1-M8, 1 case with ROS1-M12, 1 case with ROS1-M14, and 1 case with double-positive ROS1-M3 and ROS1-M8 fusion genes. The total detection rate of ALK fusion gene and ROS1 fusion gene was 7.9% (24/302) and 278 cases showed to be negative for ALK fusion gene and ROS1 fusion gene. The successful detection rates for Sanger DNA sequencing were also 100%. The positive, negative and total coincidence rates obtained by real-time fluorescent PCR and by Sanger DNA sequencing were all 100%. Conclusions: The results of Sanger DNA sequencing demonstrate that the real-time fluorescent PCR assay is equally effective in detecting ALK and ROS1 fusion genes in NSCLC tissues. Furthermore, real-time fluorescent PCR assay can be used to detect trace ALK and ROS1 fusion gene simultaneously in tiny samples, and can save time and avoid repeated sampling. It is worthy of recommendation as a rapid and reliable detection technique.

Development and validation of a real-time PCR assay for the detection of anguillid herpesvirus 1.

PubMed

van Beurden, S J; Voorbergen-Laarman, M A; Roozenburg, I; van Tellingen, J; Haenen, O L M; Engelsma, M Y

2016-01-01

Anguillid herpesvirus 1 (AngHV1) causes a haemorrhagic disease with increased mortality in wild and farmed European eel, Anguilla anguilla (L.) and Japanese eel Anguilla japonica, Temminck & Schlegel). Detection of AngHV1 is currently based on virus isolation in cell culture, antibody-based typing assays or conventional PCR. We developed, optimized and concisely validated a diagnostic TaqMan probe based real-time PCR assay for the detection of AngHV1. The primers and probe target AngHV1 open reading frame 57, encoding the capsid protease and scaffold protein. Compared to conventional PCR, the developed real-time PCR is faster, less labour-intensive and has a reduced risk of cross-contamination. The real-time PCR assay was shown to be analytically sensitive and specific and has a high repeatability, efficiency and r(2) -value. The diagnostic performance of the assay was determined by testing 10% w/v organ suspensions and virus cultures from wild and farmed European eels from the Netherlands by conventional and real-time PCR. The developed real-time PCR assay is a useful tool for the rapid and sensitive detection of AngHV1 in 10% w/v organ suspensions from wild and farmed European eels. © 2015 John Wiley & Sons Ltd.

Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing.

PubMed

Bergfors, Assar; Leenheer, Daniël; Bergqvist, Anders; Ameur, Adam; Lennerstrand, Johan

2016-02-01

Development of Hepatitis C virus (HCV) resistance against direct-acting antivirals (DAAs), including NS5A inhibitors, is an obstacle to successful treatment of HCV when DAAs are used in sub-optimal combinations. Furthermore, it has been shown that baseline (pre-existing) resistance against DAAs is present in treatment naïve-patients and this will potentially complicate future treatment strategies in different HCV genotypes (GTs). Thus the aim was to detect low levels of NS5A resistant associated variants (RAVs) in a limited sample set of treatment-naïve patients of HCV GT1a and 3a, since such polymorphisms can display in vitro resistance as high as 60000 fold. Ultra-deep single molecule real time (SMRT) sequencing with the Pacific Biosciences (PacBio) RSII instrument was used to detect these RAVs. The SMRT sequencing was conducted on ten samples; three of them positive with Sanger sequencing (GT1a Q30H and Y93N, and GT3a Y93H), five GT1a samples, and two GT3a non-positive samples. The same methods were applied to the HCV GT1a H77-plasmid in a dilution series, in order to determine the error rates of replication, which in turn was used to determine the limit of detection (LOD), as defined by mean + 3SD, of minority variants down to 0.24%. We found important baseline NS5A RAVs at levels between 0.24 and 0.5%, which could potentially have clinical relevance. This new method with low level detection of baseline RAVs could be useful in predicting the most cost-efficient combination of DAA treatment, and reduce the treatment duration for an HCV infected individual. Copyright © 2015 Elsevier B.V. All rights reserved.

Complete Genome Sequence of Clavibacter michiganensis subsp. insidiosus R1-1 Using PacBio Single-Molecule Real-Time Technology

PubMed Central

Lu, You; Samac, Deborah A.; Glazebrook, Jane

2015-01-01

We report here the complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1, isolated in Minnesota, USA. The R1-1 genome, generated by a de novo assembly of PacBio sequencing data, is the first complete genome sequence available for this subspecies. PMID:25953184

Real-time image annotation by manifold-based biased Fisher discriminant analysis

NASA Astrophysics Data System (ADS)

Ji, Rongrong; Yao, Hongxun; Wang, Jicheng; Sun, Xiaoshuai; Liu, Xianming

2008-01-01

Automatic Linguistic Annotation is a promising solution to bridge the semantic gap in content-based image retrieval. However, two crucial issues are not well addressed in state-of-art annotation algorithms: 1. The Small Sample Size (3S) problem in keyword classifier/model learning; 2. Most of annotation algorithms can not extend to real-time online usage due to their low computational efficiencies. This paper presents a novel Manifold-based Biased Fisher Discriminant Analysis (MBFDA) algorithm to address these two issues by transductive semantic learning and keyword filtering. To address the 3S problem, Co-Training based Manifold learning is adopted for keyword model construction. To achieve real-time annotation, a Bias Fisher Discriminant Analysis (BFDA) based semantic feature reduction algorithm is presented for keyword confidence discrimination and semantic feature reduction. Different from all existing annotation methods, MBFDA views image annotation from a novel Eigen semantic feature (which corresponds to keywords) selection aspect. As demonstrated in experiments, our manifold-based biased Fisher discriminant analysis annotation algorithm outperforms classical and state-of-art annotation methods (1.K-NN Expansion; 2.One-to-All SVM; 3.PWC-SVM) in both computational time and annotation accuracy with a large margin.

Real time simulation of computer-assisted sequencing of terminal area operations

NASA Technical Reports Server (NTRS)

Dear, R. G.

1981-01-01

A simulation was developed to investigate the utilization of computer assisted decision making for the task of sequencing and scheduling aircraft in a high density terminal area. The simulation incorporates a decision methodology termed Constrained Position Shifting. This methodology accounts for aircraft velocity profiles, routes, and weight classes in dynamically sequencing and scheduling arriving aircraft. A sample demonstration of Constrained Position Shifting is presented where six aircraft types (including both light and heavy aircraft) are sequenced to land at Denver's Stapleton International Airport. A graphical display is utilized and Constrained Position Shifting with a maximum shift of four positions (rearward or forward) is compared to first come, first serve with respect to arrival at the runway. The implementation of computer assisted sequencing and scheduling methodologies is investigated. A time based control concept will be required and design considerations for such a system are discussed.

Web-Based Real-Time Emergency Monitoring

NASA Technical Reports Server (NTRS)

Harvey, Craig A.; Lawhead, Joel

2007-01-01

The Web-based Real-Time Asset Monitoring (RAM) module for emergency operations and facility management enables emergency personnel in federal agencies and local and state governments to monitor and analyze data in the event of a natural disaster or other crisis that threatens a large number of people and property. The software can manage many disparate sources of data within a facility, city, or county. It was developed on industry-standard Geo- Spatial software and is compliant with open GIS standards. RAM View can function as a standalone system, or as an integrated plugin module to Emergency Operations Center (EOC) software suites such as REACT (Real-time Emergency Action Coordination Tool), thus ensuring the widest possible distribution among potential users. RAM has the ability to monitor various data sources, including streaming data. Many disparate systems are included in the initial suite of supported hardware systems, such as mobile GPS units, ambient measurements of temperature, moisture and chemical agents, flow meters, air quality, asset location, and meteorological conditions. RAM View displays real-time data streams such as gauge heights from the U.S. Geological Survey gauging stations, flood crests from the National Weather Service, and meteorological data from numerous sources. Data points are clearly visible on the map interface, and attributes as specified in the user requirements can be viewed and queried.

Direct Detection and Sequencing of Damaged DNA Bases

PubMed Central

2011-01-01

Products of various forms of DNA damage have been implicated in a variety of important biological processes, such as aging, neurodegenerative diseases, and cancer. Therefore, there exists great interest to develop methods for interrogating damaged DNA in the context of sequencing. Here, we demonstrate that single-molecule, real-time (SMRT®) DNA sequencing can directly detect damaged DNA bases in the DNA template - as a by-product of the sequencing method - through an analysis of the DNA polymerase kinetics that are altered by the presence of a modified base. We demonstrate the sequencing of several DNA templates containing products of DNA damage, including 8-oxoguanine, 8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine, 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thymine dimers, and show that these base modifications can be readily detected with single-modification resolution and DNA strand specificity. We characterize the distinct kinetic signatures generated by these DNA base modifications. PMID:22185597

Direct detection and sequencing of damaged DNA bases.

PubMed

Clark, Tyson A; Spittle, Kristi E; Turner, Stephen W; Korlach, Jonas

2011-12-20

Products of various forms of DNA damage have been implicated in a variety of important biological processes, such as aging, neurodegenerative diseases, and cancer. Therefore, there exists great interest to develop methods for interrogating damaged DNA in the context of sequencing. Here, we demonstrate that single-molecule, real-time (SMRT®) DNA sequencing can directly detect damaged DNA bases in the DNA template - as a by-product of the sequencing method - through an analysis of the DNA polymerase kinetics that are altered by the presence of a modified base. We demonstrate the sequencing of several DNA templates containing products of DNA damage, including 8-oxoguanine, 8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine, 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thymine dimers, and show that these base modifications can be readily detected with single-modification resolution and DNA strand specificity. We characterize the distinct kinetic signatures generated by these DNA base modifications.

Real-time application of knowledge-based systems

NASA Technical Reports Server (NTRS)

Brumbaugh, Randal W.; Duke, Eugene L.

1989-01-01

The Rapid Prototyping Facility (RPF) was developed to meet a need for a facility which allows flight systems concepts to be prototyped in a manner which allows for real-time flight test experience with a prototype system. This need was focused during the development and demonstration of the expert system flight status monitor (ESFSM). The ESFSM was a prototype system developed on a LISP machine, but lack of a method for progressive testing and problem identification led to an impractical system. The RPF concept was developed, and the ATMS designed to exercise its capabilities. The ATMS Phase 1 demonstration provided a practical vehicle for testing the RPF, as well as a useful tool. ATMS Phase 2 development continues. A dedicated F-18 is expected to be assigned for facility use in late 1988, with RAV modifications. A knowledge-based autopilot is being developed using the RPF. This is a system which provides elementary autopilot functions and is intended as a vehicle for testing expert system verification and validation methods. An expert system propulsion monitor is being prototyped. This system provides real-time assistance to an engineer monitoring a propulsion system during a flight.

Rapid DNA extraction protocol for detection of alpha-1 antitrypsin deficiency from dried blood spots by real-time PCR.

PubMed

Struniawski, R; Szpechcinski, A; Poplawska, B; Skronski, M; Chorostowska-Wynimko, J

2013-01-01

The dried blood spot (DBS) specimens have been successfully employed for the large-scale diagnostics of α1-antitrypsin (AAT) deficiency as an easy to collect and transport alternative to plasma/serum. In the present study we propose a fast, efficient, and cost effective protocol of DNA extraction from dried blood spot (DBS) samples that provides sufficient quantity and quality of DNA and effectively eliminates any natural PCR inhibitors, allowing for successful AAT genotyping by real-time PCR and direct sequencing. DNA extracted from 84 DBS samples from chronic obstructive pulmonary disease patients was genotyped for AAT deficiency variants by real-time PCR. The results of DBS AAT genotyping were validated by serum IEF phenotyping and AAT concentration measurement. The proposed protocol allowed successful DNA extraction from all analyzed DBS samples. Both quantity and quality of DNA were sufficient for further real-time PCR and, if necessary, for genetic sequence analysis. A 100% concordance between AAT DBS genotypes and serum phenotypes in positive detection of two major deficiency S- and Z- alleles was achieved. Both assays, DBS AAT genotyping by real-time PCR and serum AAT phenotyping by IEF, positively identified PI*S and PI*Z allele in 8 out of the 84 (9.5%) and 16 out of 84 (19.0%) patients, respectively. In conclusion, the proposed protocol noticeably reduces the costs and the hand-on-time of DBS samples preparation providing genomic DNA of sufficient quantity and quality for further real-time PCR or genetic sequence analysis. Consequently, it is ideally suited for large-scale AAT deficiency screening programs and should be method of choice.

Complete Genome Sequence of Clavibacter michiganensis subsp. insidiosus R1-1 Using PacBio Single-Molecule Real-Time Technology.

PubMed

Lu, You; Samac, Deborah A; Glazebrook, Jane; Ishimaru, Carol A

2015-05-07

We report here the complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1, isolated in Minnesota, USA. The R1-1 genome, generated by a de novo assembly of PacBio sequencing data, is the first complete genome sequence available for this subspecies. Copyright © 2015 Lu et al.

High-speed real-time OFDM transmission based on FPGA

NASA Astrophysics Data System (ADS)

Xiao, Xin; Li, Fan; Yu, Jianjun

2016-02-01

In this paper, we review our recent research progresses on real-time orthogonal frequency division multiplexing (OFDM) transmission based on FPGA. We successfully demonstrated four-channel wavelength-division multiplexing (WDM) 256.51Gb/s 16-ary quadrature amplitude modulation (16QAM)-OFDM signal transmission system for short-reach optical amplifier free inter-connection with real-time reception. Four optical carriers are modulated by four different 16QAM-OFDM signals via 10G-class direct modulation lasers (DMLs). We achieved highest capacity real-time reception optical OFDM signal transmission over 2.4-km SMF with the bit-error ratio (BER) under soft-decision forward error correction (SD-FEC) limitation of 2.4×10-2. In order to achieve higher spectrum efficiency (SE), we demonstrate 4-channel high level QAM-OFDM transmission over 20-km SMF-28 with real-time reception. 58.72-Gb/s 256QAM-OFDM and 56.4-Gb/s 128QAM-OFDM signal transmission within 25-GHz grid is achieved with the BER under 2.4×10-2 and real-time reception.

[Comparative analysis of real-time quantitative PCR-Sanger sequencing method and TaqMan probe method for detection of KRAS/BRAF mutation in colorectal carcinomas].

PubMed

Zhang, Xun; Wang, Yuehua; Gao, Ning; Wang, Jinfen

2014-02-01

To compare the application values of real-time quantitative PCR-Sanger sequencing and TaqMan probe method in the detection of KRAS and BRAF mutations, and to correlate KRAS/BRAF mutations with the clinicopathological characteristics in colorectal carcinomas. Genomic DNA of the tumor cells was extracted from formalin fixed paraffin embedded (FFPE) tissue samples of 344 colorectal carcinomas by microdissection. Real-time quantitative PCR-Sanger sequencing and TaqMan probe method were performed to detect the KRAS/BRAF mutations. The frequency and types of KRAS/BRAF mutations, clinicopathological characteristics and survival time were analyzed. KRAS mutations were detected in 39.8% (137/344) and 38.7% (133/344) of 344 colorectal carcinomas by using real-time quantitative PCR-Sanger sequencing and TaqMan probe method, respectively. BRAF mutation was detected in 4.7% (16/344) and 4.1% (14/344), respectively. There was no significant correlation between the two methods. The frequency of the KRAS mutation in female was higher than that in male (P < 0.05). The frequency of the BRAF mutation in colon was higher than that in rectum. The frequency of the BRAF mutation in stage III-IV cases was higher than that in stageI-II cases. The frequency of the BRAF mutation in signet ring cell carcinoma was higher than that in mucinous carcinoma and nonspecific adenocarcinoma had the lowest mutation rate. The frequency of the BRAF mutation in grade III cases was higher than that in grade II cases (P < 0.05). The overall concordance for the two methods of KRAS/BRAF mutation detection was 98.8% (kappa = 0.976). There was statistic significance between BRAF and KRAS mutations for the survival time of colorectal carcinomas (P = 0.039). There were no statistic significance between BRAF mutation type and BRAF/KRAS wild type (P = 0.058). (1) Compared with real-time quantitative PCR-Sanger sequencing, TaqMan probe method is better with regard to handling time, efficiency, repeatability, cost

Species level identification of coagulase negative Staphylococcus spp. from buffalo using matrix-assisted laser desorption ionization-time of flight mass spectrometry and cydB real-time quantitative PCR.

PubMed

Pizauro, Lucas J L; de Almeida, Camila C; Soltes, Glenn A; Slavic, Durda; Rossi-Junior, Oswaldo D; de Ávila, Fernando A; Zafalon, Luiz F; MacInnes, Janet I

2017-05-01

Incorrect identification of Staphylococcus spp. can have serious clinical and zoonotic repercussions. Accordingly, the aim of this study was to determine if matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and/or cydB real- time quantitative PCR (qPCR) could be used to accurately identify coagulase negative Staphylococcus spp. (CoNS) obtained from buffalo milk and milking environment samples. Seventy-five of 84 CoNS isolates could be identified to the species level (score value >1.99) using MALDI-TOF MS. However, as determined by cytochrome d ubiquinol oxidase subunit II (cydB) qPCR and by 16S RNA and cydB gene sequencing, 10S. agnetis strains were wrongly identified as S. hyicus by MALDI-TOF MS. In addition, 9 isolates identified by MALDI-TOF only to the genus level (score values between 1.70 and 1.99) could be identified to species by cydB qPCR. Our findings suggest that MALDI-TOF MS is a reliable method for rapid identification of S. chromogenes and S. epidermidis (species of interest both in human and veterinary medicine) and may be able to correctly identify other Staphylococcus spp. However, at present not all Staphylococcus spp. found in buffalo milk can be accurately identified by MALDI-TOF MS and for these organisms, the cydB qPCR developed in the current study may provide a reliable alternative method for rapid identification of CoNS species. Copyright © 2017 Elsevier B.V. All rights reserved.

Reasoning about real-time systems with temporal interval logic constraints on multi-state automata

NASA Technical Reports Server (NTRS)

Gabrielian, Armen

1991-01-01

Models of real-time systems using a single paradigm often turn out to be inadequate, whether the paradigm is based on states, rules, event sequences, or logic. A model-based approach to reasoning about real-time systems is presented in which a temporal interval logic called TIL is employed to define constraints on a new type of high level automata. The combination, called hierarchical multi-state (HMS) machines, can be used to model formally a real-time system, a dynamic set of requirements, the environment, heuristic knowledge about planning-related problem solving, and the computational states of the reasoning mechanism. In this framework, mathematical techniques were developed for: (1) proving the correctness of a representation; (2) planning of concurrent tasks to achieve goals; and (3) scheduling of plans to satisfy complex temporal constraints. HMS machines allow reasoning about a real-time system from a model of how truth arises instead of merely depending of what is true in a system.

Human action recognition based on kinematic similarity in real time

PubMed Central

Chen, Longting; Luo, Ailing; Zhang, Sicong

2017-01-01

Human action recognition using 3D pose data has gained a growing interest in the field of computer robotic interfaces and pattern recognition since the availability of hardware to capture human pose. In this paper, we propose a fast, simple, and powerful method of human action recognition based on human kinematic similarity. The key to this method is that the action descriptor consists of joints position, angular velocity and angular acceleration, which can meet the different individual sizes and eliminate the complex normalization. The angular parameters of joints within a short sliding time window (approximately 5 frames) around the current frame are used to express each pose frame of human action sequence. Moreover, three modified KNN (k-nearest-neighbors algorithm) classifiers are employed in our method: one for achieving the confidence of every frame in the training step, one for estimating the frame label of each descriptor, and one for classifying actions. Additional estimating of the frame’s time label makes it possible to address single input frames. This approach can be used on difficult, unsegmented sequences. The proposed method is efficient and can be run in real time. The research shows that many public datasets are irregularly segmented, and a simple method is provided to regularize the datasets. The approach is tested on some challenging datasets such as MSR-Action3D, MSRDailyActivity3D, and UTD-MHAD. The results indicate our method achieves a higher accuracy. PMID:29073131

GNSS global real-time augmentation positioning: Real-time precise satellite clock estimation, prototype system construction and performance analysis

NASA Astrophysics Data System (ADS)

Chen, Liang; Zhao, Qile; Hu, Zhigang; Jiang, Xinyuan; Geng, Changjiang; Ge, Maorong; Shi, Chuang

2018-01-01

Lots of ambiguities in un-differenced (UD) model lead to lower calculation efficiency, which isn't appropriate for the high-frequency real-time GNSS clock estimation, like 1 Hz. Mixed differenced model fusing UD pseudo-range and epoch-differenced (ED) phase observations has been introduced into real-time clock estimation. In this contribution, we extend the mixed differenced model for realizing multi-GNSS real-time clock high-frequency updating and a rigorous comparison and analysis on same conditions are performed to achieve the best real-time clock estimation performance taking the efficiency, accuracy, consistency and reliability into consideration. Based on the multi-GNSS real-time data streams provided by multi-GNSS Experiment (MGEX) and Wuhan University, GPS + BeiDou + Galileo global real-time augmentation positioning prototype system is designed and constructed, including real-time precise orbit determination, real-time precise clock estimation, real-time Precise Point Positioning (RT-PPP) and real-time Standard Point Positioning (RT-SPP). The statistical analysis of the 6 h-predicted real-time orbits shows that the root mean square (RMS) in radial direction is about 1-5 cm for GPS, Beidou MEO and Galileo satellites and about 10 cm for Beidou GEO and IGSO satellites. Using the mixed differenced estimation model, the prototype system can realize high-efficient real-time satellite absolute clock estimation with no constant clock-bias and can be used for high-frequency augmentation message updating (such as 1 Hz). The real-time augmentation message signal-in-space ranging error (SISRE), a comprehensive accuracy of orbit and clock and effecting the users' actual positioning performance, is introduced to evaluate and analyze the performance of GPS + BeiDou + Galileo global real-time augmentation positioning system. The statistical analysis of real-time augmentation message SISRE is about 4-7 cm for GPS, whlile 10 cm for Beidou IGSO/MEO, Galileo and about 30 cm

Flanking sequence determination and specific PCR identification of transgenic wheat B102-1-2.

PubMed

Cao, Jijuan; Xu, Junyi; Zhao, Tongtong; Cao, Dongmei; Huang, Xin; Zhang, Piqiao; Luan, Fengxia

2014-01-01

The exogenous fragment sequence and flanking sequence between the exogenous fragment and recombinant chromosome of transgenic wheat B102-1-2 were successfully acquired using genome walking technology. The newly acquired exogenous fragment encoded the full-length sequence of transformed genes with transformed plasmid and corresponding functional genes including ubi, vector pBANF-bar, vector pUbiGUSPlus, vector HSP, reporter vector pUbiGUSPlus, promoter ubiquitin, and coli DH1. A specific polymerase chain reaction (PCR) identification method for transgenic wheat B102-1-2 was established on the basis of designed primers according to flanking sequence. This established specific PCR strategy was validated by using transgenic wheat, transgenic corn, transgenic soybean, transgenic rice, and non-transgenic wheat. A specifically amplified target band was observed only in transgenic wheat B102-1-2. Therefore, this method is characterized by high specificity, high reproducibility, rapid identification, and excellent accuracy for the identification of transgenic wheat B102-1-2.

Characterization of Samples Identified as Hepatitis C Virus Genotype 1 without Subtype by Abbott RealTime HCV Genotype II Assay Using the New Abbott HCV Genotype Plus RUO Test.

PubMed

Mokhtari, Camelia; Ebel, Anne; Reinhardt, Birgit; Merlin, Sandra; Proust, Stéphanie; Roque-Afonso, Anne-Marie

2016-02-01

Hepatitis C virus (HCV) genotyping continues to be relevant for therapeutic strategies. Some samples are reported as genotype 1 (gt 1) without subtype by the Abbott RealTime HCV Genotype II (GT II) test. To characterize such samples further, the Abbott HCV Genotype Plus RUO (Plus) assay, which targets the core region for gt 1a, gt 1b, and gt 6 detection, was evaluated as a reflex test in reference to NS5B or 5'-untranslated region (UTR)/core region sequencing. Of 3,626 routine samples, results of gt 1 without subtype were received for 171 samples (4.7%), accounting for 11.5% of gt 1 specimens. The Plus assay and sequencing were applied to 98 of those samples. NS5B or 5'-UTR/core region sequencing was successful for 91/98 specimens (92.9%). Plus assay and sequencing results were concordant for 87.9% of specimens (80/91 samples). Sequencing confirmed Plus assay results for 82.6%, 85.7%, 100%, and 89.3% of gt 1a, gt 1b, gt 6, and non-gt 1a/1b/6 results, respectively. Notably, 12 gt 6 samples that had been identified previously as gt 1 without subtype were assigned correctly here; for 25/28 samples reported as "not detected" by the Plus assay, sequencing identified the samples as gt 1 with subtypes other than 1a/1b. The genetic variability of HCV continues to present challenges for the current genotyping platforms regardless of the applied methodology. Samples identified by the GT II assay as gt 1 without subtype can be further resolved and reliably characterized by the new Plus assay. Copyright © 2016 Mokhtari et al.

A real-time ionospheric model based on GNSS Precise Point Positioning

NASA Astrophysics Data System (ADS)

Tu, Rui; Zhang, Hongping; Ge, Maorong; Huang, Guanwen

2013-09-01

This paper proposes a method of real-time monitoring and modeling the ionospheric Total Electron Content (TEC) by Precise Point Positioning (PPP). Firstly, the ionospheric TEC and receiver’s Differential Code Biases (DCB) are estimated with the undifferenced raw observation in real-time, then the ionospheric TEC model is established based on the Single Layer Model (SLM) assumption and the recovered ionospheric TEC. In this study, phase observations with high precision are directly used instead of phase smoothed code observations. In addition, the DCB estimation is separated from the establishment of the ionospheric model which will limit the impacts of the SLM assumption impacts. The ionospheric model is established at every epoch for real time application. The method is validated with three different GNSS networks on a local, regional, and global basis. The results show that the method is feasible and effective, the real-time ionosphere and DCB results are very consistent with the IGS final products, with a bias of 1-2 TECU and 0.4 ns respectively.

Application of a molecular beacon based real-time isothermal amplification (MBRTIA) technology for simultaneous detection of Bacillus cereus and Staphylococcus aureus.

PubMed

Mandappa, I M; Joglekar, Prasanna; Manonmani, H K

2015-07-01

A multiplex real-time isothermal amplification assay was developed using molecular beacons for the detection of Bacillus cereus and Staphylococcus aureus by targeting four important virulence genes. A correlation between targeting highly accessible DNA sequences and isothermal amplification based molecular beacon efficiency and sensitivity was demonstrated using phi(Φ)29 DNA polymerase at a constant isothermal temperature of 30 °C. It was very selective and consistently detected down to 10(1) copies of DNA. The specificity and sensitivity of this assay, when tested with pure culture were high, surpassing those of currently used PCR assays for the detection of these organisms. The molecular beacon based real-time isothermal amplification (MBRTIA) assay could be carried out entirely in 96 well plates or well strips, enabling a rapid and high-throughput detection of food borne pathogens.

A Microprocessor-Based Real-Time Simulator of a Turbofan Engine

DTIC Science & Technology

1988-01-01

NASA AVSCOM Technical Memorandum 100889 Technical Report 88-C-011 Lfl A Microprocessor-Based Real-Time Simulator of a Turbofan Engine CD I Jonathan S...Accession For NTIS GRA&I A MICROPROCESSOR-BASED REAL-TIME SIMULATOR DTIC TABUnannounced OF A TURBOFAN ENGINE Justifiaation, Jonathan S. Litt Propulsion...the F100 engine without augmentation (without afterburning). HYTESS is a simplified simulation written in FORTRAN of a generalized turbofan engine . To

Real Time Radiation Monitoring Using Nanotechnology

NASA Technical Reports Server (NTRS)

Li, Jing (Inventor); Hanratty, James J. (Inventor); Wilkins, Richard T. (Inventor); Lu, Yijiang (Inventor)

2016-01-01

System and method for monitoring receipt and estimating flux value, in real time, of incident radiation, using two or more nanostructures (NSs) and associated terminals to provide closed electrical paths and to measure one or more electrical property change values .DELTA.EPV, associated with irradiated NSs, during a sequence of irradiation time intervals. Effects of irradiation, without healing and with healing, of the NSs, are separately modeled for first order and second order healing. Change values.DELTA.EPV are related to flux, to cumulative dose received by NSs, and to radiation and healing effectivity parameters and/or.mu., associated with the NS material and to the flux. Flux and/or dose are estimated in real time, based on EPV change values, using measured .DELTA.EPV values. Threshold dose for specified changes of biological origin (usually undesired) can be estimated. Effects of time-dependent radiation flux are analyzed in pre-healing and healing regimes.

Real-time cardiovascular magnetic resonance at 1.5 T using balanced SSFP and 40 ms resolution

PubMed Central

2013-01-01

Background While cardiovascular magnetic resonance (CMR) commonly employs ECG-synchronized cine acquisitions with balanced steady-state free precession (SSFP) contrast at 1.5 T, recent developments at 3 T demonstrate significant potential for T1-weighted real-time imaging at high spatiotemporal resolution using undersampled radial FLASH. The purpose of this work was to combine both ideas and to evaluate a corresponding real-time CMR method at 1.5 T with SSFP contrast. Methods Radial gradient-echo sequences with fully balanced gradients and at least 15-fold undersampling were implemented on two CMR systems with different gradient performance. Image reconstruction by regularized nonlinear inversion (NLINV) was performed offline and resulted in real-time SSFP CMR images at a nominal resolution of 1.8 mm and with acquisition times of 40 ms. Results Studies of healthy subjects demonstrated technical feasibility in terms of robustness and general image quality. Clinical applicability with access to quantitative evaluations (e.g., ejection fraction) was confirmed by preliminary applications to 27 patients with typical indications for CMR including arrhythmias and abnormal wall motion. Real-time image quality was slightly lower than for cine SSFP recordings, but considered diagnostic in all cases. Conclusions Extending conventional cine approaches, real-time radial SSFP CMR with NLINV reconstruction provides access to individual cardiac cycles and allows for studies of patients with irregular heartbeat. PMID:24028285

B-Bolivia, an Allele of the Maize b1 Gene with Variable Expression, Contains a High Copy Retrotransposon-Related Sequence Immediately Upstream1

PubMed Central

Selinger, David A.; Chandler, Vicki L.

2001-01-01

The maize (Zea mays) b1 gene encodes a transcription factor that regulates the anthocyanin pigment pathway. Of the b1 alleles with distinct tissue-specific expression, B-Peru and B-Bolivia are the only alleles that confer seed pigmentation. B-Bolivia produces variable and weaker seed expression but darker, more regular plant expression relative to B-Peru. Our experiments demonstrated that B-Bolivia is not expressed in the seed when transmitted through the male. When transmitted through the female the proportion of kernels pigmented and the intensity of pigment varied. Molecular characterization of B-Bolivia demonstrated that it shares the first 530 bp of the upstream region with B-Peru, a region sufficient for seed expression. Immediately upstream of 530 bp, B-Bolivia is completely divergent from B-Peru. These sequences share sequence similarity to retrotransposons. Transient expression assays of various promoter constructs identified a 33-bp region in B-Bolivia that can account for the reduced aleurone pigment amounts (40%) observed with B-Bolivia relative to B-Peru. Transgenic plants carrying the B-Bolivia promoter proximal region produced pigmented seeds. Similar to native B-Bolivia, some transgene loci are variably expressed in seeds. In contrast to native B-Bolivia, the transgene loci are expressed in seeds when transmitted through both the male and female. Some transgenic lines produced pigment in vegetative tissues, but the tissue-specificity was different from B-Bolivia, suggesting the introduced sequences do not contain the B-Bolivia plant-specific regulatory sequences. We hypothesize that the chromatin context of the B-Bolivia allele controls its epigenetic seed expression properties, which could be influenced by the adjacent highly repeated retrotransposon sequence. PMID:11244116

Comparative evaluation of the performance of the Abbott RealTime HIV-1 assay for measurement of HIV-1 plasma viral load on genetically diverse samples from Greece

PubMed Central

2011-01-01

Background HIV-1 is characterized by increased genetic heterogeneity which tends to hinder the reliability of detection and accuracy of HIV-1 RNA quantitation assays. Methods In this study, the Abbott RealTime HIV-1 (Abbott RealTime) assay was compared to the Roche Cobas TaqMan HIV-1 (Cobas TaqMan) and the Siemens Versant HIV-1 RNA 3.0 (bDNA 3.0) assays, using clinical samples of various viral load levels and subtypes from Greece, where the recent epidemiology of HIV-1 infection has been characterized by increasing genetic diversity and a marked increase in subtype A genetic strains among newly diagnosed infections. Results A high correlation was observed between the quantitative results obtained by the Abbott RealTime and the Cobas TaqMan assays. Viral load values quantified by the Abbott RealTime were on average lower than those obtained by the Cobas TaqMan, with a mean (SD) difference of -0.206 (0.298) log10 copies/ml. The mean differences according to HIV-1 subtypes between the two techniques for samples of subtype A, B, and non-A/non-B were 0.089, -0.262, and -0.298 log10 copies/ml, respectively. Overall, differences were less than 0.5 log10 for 85% of the samples, and >1 log10 in only one subtype B sample. Similarly, Abbott RealTime and bDNA 3.0 assays yielded a very good correlation of quantitative results, whereas viral load values assessed by the Abbott RealTime were on average higher (mean (SD) difference: 0.160 (0.287) log10 copies/ml). The mean differences according to HIV-1 subtypes between the two techniques for subtype A, B and non-A/non-B samples were 0.438, 0.105 and 0.191 log10 copies/ml, respectively. Overall, the majority of samples (86%) differed by less than 0.5 log10, while none of the samples showed a deviation of more than 1.0 log10. Conclusions In an area of changing HIV-1 subtype pattern, the Abbott RealTime assay showed a high correlation and good agreement of results when compared both to the Cobas TaqMan and bDNA 3.0 assays, for all

Real-Time PCR Typing of Escherichia coli Based on Multiple Single Nucleotide Polymorphisms--a Convenient and Rapid Method.

PubMed

Lager, Malin; Mernelius, Sara; Löfgren, Sture; Söderman, Jan

2016-01-01

Healthcare-associated infections caused by Escherichia coli and antibiotic resistance due to extended-spectrum beta-lactamase (ESBL) production constitute a threat against patient safety. To identify, track, and control outbreaks and to detect emerging virulent clones, typing tools of sufficient discriminatory power that generate reproducible and unambiguous data are needed. A probe based real-time PCR method targeting multiple single nucleotide polymorphisms (SNP) was developed. The method was based on the multi locus sequence typing scheme of Institute Pasteur and by adaptation of previously described typing assays. An 8 SNP-panel that reached a Simpson's diversity index of 0.95 was established, based on analysis of sporadic E. coli cases (ESBL n = 27 and non-ESBL n = 53). This multi-SNP assay was used to identify the sequence type 131 (ST131) complex according to the Achtman's multi locus sequence typing scheme. However, it did not fully discriminate within the complex but provided a diagnostic signature that outperformed a previously described detection assay. Pulsed-field gel electrophoresis typing of isolates from a presumed outbreak (n = 22) identified two outbreaks (ST127 and ST131) and three different non-outbreak-related isolates. Multi-SNP typing generated congruent data except for one non-outbreak-related ST131 isolate. We consider multi-SNP real-time PCR typing an accessible primary generic E. coli typing tool for rapid and uniform type identification.

A system for EPID-based real-time treatment delivery verification during dynamic IMRT treatment.

PubMed

Fuangrod, Todsaporn; Woodruff, Henry C; van Uytven, Eric; McCurdy, Boyd M C; Kuncic, Zdenka; O'Connor, Daryl J; Greer, Peter B

2013-09-01

To design and develop a real-time electronic portal imaging device (EPID)-based delivery verification system for dynamic intensity modulated radiation therapy (IMRT) which enables detection of gross treatment delivery errors before delivery of substantial radiation to the patient. The system utilizes a comprehensive physics-based model to generate a series of predicted transit EPID image frames as a reference dataset and compares these to measured EPID frames acquired during treatment. The two datasets are using MLC aperture comparison and cumulative signal checking techniques. The system operation in real-time was simulated offline using previously acquired images for 19 IMRT patient deliveries with both frame-by-frame comparison and cumulative frame comparison. Simulated error case studies were used to demonstrate the system sensitivity and performance. The accuracy of the synchronization method was shown to agree within two control points which corresponds to approximately ∼1% of the total MU to be delivered for dynamic IMRT. The system achieved mean real-time gamma results for frame-by-frame analysis of 86.6% and 89.0% for 3%, 3 mm and 4%, 4 mm criteria, respectively, and 97.9% and 98.6% for cumulative gamma analysis. The system can detect a 10% MU error using 3%, 3 mm criteria within approximately 10 s. The EPID-based real-time delivery verification system successfully detected simulated gross errors introduced into patient plan deliveries in near real-time (within 0.1 s). A real-time radiation delivery verification system for dynamic IMRT has been demonstrated that is designed to prevent major mistreatments in modern radiation therapy.

Profiling of Oral Microbiota in Early Childhood Caries Using Single-Molecule Real-Time Sequencing.

PubMed

Wang, Yuan; Zhang, Jie; Chen, Xi; Jiang, Wen; Wang, Sa; Xu, Lei; Tu, Yan; Zheng, Pei; Wang, Ying; Lin, Xiaolong; Chen, Hui

2017-01-01

Background: Alterations of oral microbiota are the main cause of the progression of caries. The goal of this study was to characterize the oral microbiota in childhood caries based on single-molecule real-time sequencing. Methods: A total of 21 preschoolers, aged 3-5 years old with severe early childhood caries, and 20 age-matched, caries-free children as controls were recruited. Saliva samples were collected, followed by DNA extraction, Pacbio sequencing, and phylogenetic analyses of the oral microbial communities. Results: Eight hundred and seventy six species derived from 13 known bacterial phyla and 110 genera were detected from 41 children using Pacbio sequencing. At the species level, 38 species, including Veillonella spp., Streptococcus spp., Prevotella spp., and Lactobacillus spp., showed higher abundance in the caries group compared to the caries-free group ( p < 0.05). The core microbiota at the genus and species levels was more stable in the caries-free micro-ecological niche. At follow-up, oral examinations 6 months after sample collection, development of new dental caries was observed in 5 children (the transitional group) among the 21 caries free children. Compared with the caries-free children, in the transitional and caries groups, 6 species, which were more abundant in the caries-free group, exhibited a relatively low abundance in both the caries group and the transitional group ( p < 0.05). We conclude that Abiotrophia spp., Neisseria spp., and Veillonella spp., might be associated with healthy oral microbial ecosystem. Prevotella spp., Lactobacillus spp., Dialister spp., and Filifactor spp. may be related to the pathogenesis and progression of dental caries.

Accident diagnosis system based on real-time decision tree expert system

NASA Astrophysics Data System (ADS)

Nicolau, Andressa dos S.; Augusto, João P. da S. C.; Schirru, Roberto

2017-06-01

Safety is one of the most studied topics when referring to power stations. For that reason, sensors and alarms develop an important role in environmental and human protection. When abnormal event happens, it triggers a chain of alarms that must be, somehow, checked by the control room operators. In this case, diagnosis support system can help operators to accurately identify the possible root-cause of the problem in short time. In this article, we present a computational model of a generic diagnose support system based on artificial intelligence, that was applied on the dataset of two real power stations: Angra1 Nuclear Power Plant and Santo Antônio Hydroelectric Plant. The proposed system processes all the information logged in the sequence of events before a shutdown signal using the expert's knowledge inputted into an expert system indicating the chain of events, from the shutdown signal to its root-cause. The results of both applications showed that the support system is a potential tool to help the control room operators identify abnormal events, as accidents and consequently increase the safety.

Real-time CT-video registration for continuous endoscopic guidance

NASA Astrophysics Data System (ADS)

Merritt, Scott A.; Rai, Lav; Higgins, William E.

2006-03-01

Previous research has shown that CT-image-based guidance could be useful for the bronchoscopic assessment of lung cancer. This research drew upon the registration of bronchoscopic video images to CT-based endoluminal renderings of the airway tree. The proposed methods either were restricted to discrete single-frame registration, which took several seconds to complete, or required non-real-time buffering and processing of video sequences. We have devised a fast 2D/3D image registration method that performs single-frame CT-Video registration in under 1/15th of a second. This allows the method to be used for real-time registration at full video frame rates without significantly altering the physician's behavior. The method achieves its speed through a gradient-based optimization method that allows most of the computation to be performed off-line. During live registration, the optimization iteratively steps toward the locally optimal viewpoint at which a CT-based endoluminal view is most similar to a current bronchoscopic video frame. After an initial registration to begin the process (generally done in the trachea for bronchoscopy), subsequent registrations are performed in real-time on each incoming video frame. As each new bronchoscopic video frame becomes available, the current optimization is initialized using the previous frame's optimization result, allowing continuous guidance to proceed without manual re-initialization. Tests were performed using both synthetic and pre-recorded bronchoscopic video. The results show that the method is robust to initialization errors, that registration accuracy is high, and that continuous registration can proceed on real-time video at >15 frames per sec. with minimal user-intervention.

NOAA’s Physical Oceanographic Real-Time Systems (PORTS(Registered))

DTIC Science & Technology

2010-06-01

1 NOAA’s Physical Oceanographic Real - Time Systems (PORTS®) Darren Wright and Robert Bassett National Oceanic and Atmospheric Administration...operation of several Physical Oceanographic Real - Time Systems (PORTS®). 0-933957-38-1 ©2009 MTS Report Documentation Page Form ApprovedOMB No. 0704-0188...TITLE AND SUBTITLE NOAAs Physical Oceanographic Real - Time Systems (PORTS®) 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6

GeneSCF: a real-time based functional enrichment tool with support for multiple organisms.

PubMed

Subhash, Santhilal; Kanduri, Chandrasekhar

2016-09-13

High-throughput technologies such as ChIP-sequencing, RNA-sequencing, DNA sequencing and quantitative metabolomics generate a huge volume of data. Researchers often rely on functional enrichment tools to interpret the biological significance of the affected genes from these high-throughput studies. However, currently available functional enrichment tools need to be updated frequently to adapt to new entries from the functional database repositories. Hence there is a need for a simplified tool that can perform functional enrichment analysis by using updated information directly from the source databases such as KEGG, Reactome or Gene Ontology etc. In this study, we focused on designing a command-line tool called GeneSCF (Gene Set Clustering based on Functional annotations), that can predict the functionally relevant biological information for a set of genes in a real-time updated manner. It is designed to handle information from more than 4000 organisms from freely available prominent functional databases like KEGG, Reactome and Gene Ontology. We successfully employed our tool on two of published datasets to predict the biologically relevant functional information. The core features of this tool were tested on Linux machines without the need for installation of more dependencies. GeneSCF is more reliable compared to other enrichment tools because of its ability to use reference functional databases in real-time to perform enrichment analysis. It is an easy-to-integrate tool with other pipelines available for downstream analysis of high-throughput data. More importantly, GeneSCF can run multiple gene lists simultaneously on different organisms thereby saving time for the users. Since the tool is designed to be ready-to-use, there is no need for any complex compilation and installation procedures.

Evaluation of Real-Time Ground-Based GPS Meteorology

NASA Astrophysics Data System (ADS)

Fang, P.; Bock, Y.; Gutman, S.

2003-04-01

We demonstrate and evaluate a system to estimate zenith tropospheric delays in real time (5-10 minute latency) based on the technique of instantaneous GPS positioning as described by Bock et al. [2000] using data from the Orange County Real Time GPS Network. OCRTN is an upgrade of a sub-network of SCIGN sites in southern California to low latency (1-2 sec), high-rate (1 Hz) data streaming. Currently, ten sites are streaming data (Ashtech binary MBEN format) by means of dedicated, point-to-point radio modems to a network hub that translates the asynchronous serial data to TCP/IP and onto a PC workstation residing on a local area network. Software residing on the PC allows multiple clients to access the raw data simultaneously though TCP/IP. One of the clients is a Geodetics RTD server that receives and archives (1) the raw 1 Hz network data, (2) estimates of instantaneous positions and zenith tropospheric delays, and (3) RINEX data to decimated to 30 seconds. The network is composed of ten sites. The distribution of nine of the sites approximates a right triangle with two 60 km legs, and a tenth site on Catalina Island a distance of about 50 km (over water) from the hypotenuse of the triangle. Relative zenith delays are estimated every second with a latency less than a second. Median values are computed at a user-specified interval (e.g., 10 minutes) with outliers greater than 4 times the interquartile range rejected. We describe the results with those generated by our operational system using the GAMIT software, with a latency of 30-60 minutes. Earlier results (from a similar network) comparing 30-minute median RTD values to GAMIT 30-minute estimates indicate that the two solutions differ by about 1 cm. We also describe our approach to determining absolute zenith delays. If an Internet connection is available we will present a real-time demonstration. [Bock, Y., R. Nikolaidis, P. J. de Jonge, and M. Bevis, Instantaneous resolution of crustal motion at medium

Detection by real-time PCR and pyrosequencing of the cry1Ab and cry1Ac genes introduced in genetically modified (GM) constructs.

PubMed

Debode, Frederic; Janssen, Eric; Bragard, Claude; Berben, Gilbert

2017-08-01

The presence of genetically modified organisms (GMOs) in food and feed is mainly detected by the use of targets focusing on promoters and terminators. As some genes are frequently used in genetically modified (GM) construction, they also constitute excellent screening elements and their use is increasing. In this paper we propose a new target for the detection of cry1Ab and cry1Ac genes by real-time polymerase chain reaction (PCR) and pyrosequencing. The specificity, sensitivity and robustness of the real-time PCR method were tested following the recommendations of international guidelines and the method met the expected performance criteria. This paper also shows how the robustness testing was assessed. This new cry1Ab/Ac method can provide a positive signal with a larger number of GM events than do the other existing methods using double dye-probes. The method permits the analysis of results with less ambiguity than the SYBRGreen method recommended by the European Reference Laboratory (EURL) GM Food and Feed (GMFF). A pyrosequencing method was also developed to gain additional information thanks to the sequence of the amplicon. This method of sequencing-by-synthesis can determine the sequence between the primers used for PCR. Pyrosequencing showed that the sequences internal to the primers present differences following the GM events considered and three different sequences were observed. The sensitivity of the pyrosequencing was tested on reference flours with a low percentage GM content and different copy numbers. Improvements in the pyrosequencing protocol provided correct sequences with 50 copies of the target. Below this copy number, the quality of the sequence was more random.

Reengineering Real-Time Software Systems

DTIC Science & Technology

1993-09-09

reengineering existing large-scale (or real-time) systems; systems designed prior to or during the advent of applied SE (Parnas 1979, Freeman 1980). Is... Advisor : Yutaka Kanayama Approved for public release; distribution is unlimited. 93-29769 93 12 6 098 Form Appmoved REPORT DOCUMENTATION PAGE 1o No. PI rep...trm b Idn 1o tl# caik t al wdornon s easnated to waere 1how per response. fr4ikcdm the time rem matnodons. siauide exetig da"a siuo a i and mami diqw

A GPS-based Real-time Road Traffic Monitoring System

NASA Astrophysics Data System (ADS)

Tanti, Kamal Kumar

In recent years, monitoring systems are astonishingly inclined towards ever more automatic; reliably interconnected, distributed and autonomous operation. Specifically, the measurement, logging, data processing and interpretation activities may be carried out by separate units at different locations in near real-time. The recent evolution of mobile communication devices and communication technologies has fostered a growing interest in the GIS & GPS-based location-aware systems and services. This paper describes a real-time road traffic monitoring system based on integrated mobile field devices (GPS/GSM/IOs) working in tandem with advanced GIS-based application software providing on-the-fly authentications for real-time monitoring and security enhancement. The described system is developed as a fully automated, continuous, real-time monitoring system that employs GPS sensors and Ethernet and/or serial port communication techniques are used to transfer data between GPS receivers at target points and a central processing computer. The data can be processed locally or remotely based on the requirements of client’s satisfaction. Due to the modular architecture of the system, other sensor types may be supported with minimal effort. Data on the distributed network & measurements are transmitted via cellular SIM cards to a Control Unit, which provides for post-processing and network management. The Control Unit may be remotely accessed via an Internet connection. The new system will not only provide more consistent data about the road traffic conditions but also will provide methods for integrating with other Intelligent Transportation Systems (ITS). For communication between the mobile device and central monitoring service GSM technology is used. The resulting system is characterized by autonomy, reliability and a high degree of automation.

Real-time traffic sign recognition based on a general purpose GPU and deep-learning.

PubMed

Lim, Kwangyong; Hong, Yongwon; Choi, Yeongwoo; Byun, Hyeran

2017-01-01

We present a General Purpose Graphics Processing Unit (GPGPU) based real-time traffic sign detection and recognition method that is robust against illumination changes. There have been many approaches to traffic sign recognition in various research fields; however, previous approaches faced several limitations when under low illumination or wide variance of light conditions. To overcome these drawbacks and improve processing speeds, we propose a method that 1) is robust against illumination changes, 2) uses GPGPU-based real-time traffic sign detection, and 3) performs region detecting and recognition using a hierarchical model. This method produces stable results in low illumination environments. Both detection and hierarchical recognition are performed in real-time, and the proposed method achieves 0.97 F1-score on our collective dataset, which uses the Vienna convention traffic rules (Germany and South Korea).

Real-time traffic sign recognition based on a general purpose GPU and deep-learning

PubMed Central

Hong, Yongwon; Choi, Yeongwoo; Byun, Hyeran

2017-01-01

We present a General Purpose Graphics Processing Unit (GPGPU) based real-time traffic sign detection and recognition method that is robust against illumination changes. There have been many approaches to traffic sign recognition in various research fields; however, previous approaches faced several limitations when under low illumination or wide variance of light conditions. To overcome these drawbacks and improve processing speeds, we propose a method that 1) is robust against illumination changes, 2) uses GPGPU-based real-time traffic sign detection, and 3) performs region detecting and recognition using a hierarchical model. This method produces stable results in low illumination environments. Both detection and hierarchical recognition are performed in real-time, and the proposed method achieves 0.97 F1-score on our collective dataset, which uses the Vienna convention traffic rules (Germany and South Korea). PMID:28264011

Tensor body: real-time reconstruction of the human body and avatar synthesis from RGB-D.

PubMed

Barmpoutis, Angelos

2013-10-01

Real-time 3-D reconstruction of the human body has many applications in anthropometry, telecommunications, gaming, fashion, and other areas of human-computer interaction. In this paper, a novel framework is presented for reconstructing the 3-D model of the human body from a sequence of RGB-D frames. The reconstruction is performed in real time while the human subject moves arbitrarily in front of the camera. The method employs a novel parameterization of cylindrical-type objects using Cartesian tensor and b-spline bases along the radial and longitudinal dimension respectively. The proposed model, dubbed tensor body, is fitted to the input data using a multistep framework that involves segmentation of the different body regions, robust filtering of the data via a dynamic histogram, and energy-based optimization with positive-definite constraints. A Riemannian metric on the space of positive-definite tensor splines is analytically defined and employed in this framework. The efficacy of the presented methods is demonstrated in several real-data experiments using the Microsoft Kinect sensor.

A Lecture Supporting System Based on Real-Time Learning Analytics

ERIC Educational Resources Information Center

Shimada, Atsushi; Konomi, Shin'ichi

2017-01-01

A new lecture supporting system based on real-time learning analytics is proposed. Our target is on-site classrooms where teachers give their lectures, and a lot of students listen to teachers' explanation, conduct exercises etc. We utilize not only an e-Learning system, but also an e-Book system to collect real-time learning activities during the…

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.

PubMed

Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

2015-08-01

RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of [Formula: see text]. Subsequently, numerous faster 'Sankoff-style' approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity ([Formula: see text] quartic time). Breaking this barrier, we introduce the novel Sankoff-style algorithm 'sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)', which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff's original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. © The Author 2015. Published by Oxford University Press.

Performance characteristics and comparison of Abbott and artus real-time systems for hepatitis B virus DNA quantification.

PubMed

Ismail, Ashrafali M; Sivakumar, Jayashree; Anantharam, Raghavendran; Dayalan, Sujitha; Samuel, Prasanna; Fletcher, Gnanadurai J; Gnanamony, Manu; Abraham, Priya

2011-09-01

Virological monitoring of hepatitis B virus (HBV) DNA is critical to the management of HBV infection. With several HBV DNA quantification assays available, it is important to use the most efficient testing system for virological monitoring. In this study, we evaluated the performance characteristics and comparability of three HBV DNA quantification systems: Abbott HBV real-time PCR (Abbott PCR), artus HBV real-time PCR with QIAamp DNA blood kit purification (artus-DB), and artus HBV real-time PCR with the QIAamp DSP virus kit purification (artus-DSP). The lower limits of detection of these systems were established against the WHO international standards for HBV DNA and were found to be 1.43, 82, and 9 IU/ml, respectively. The intra-assay and interassay coefficients of variation of plasma samples (1 to 6 log(10) IU/ml) ranged between 0.05 to 8.34% and 0.16 to 3.48% for the Abbott PCR, 1.53 to 26.85% and 0.50 to 12.89% for artus-DB, and 0.29 to 7.42% and 0.94 to 3.01% for artus-DSP, respectively. Ninety HBV clinical samples were used for comparison of assays, and paired quantitative results showed strong correlation by linear regression analysis (artus-DB with Abbott PCR, r = 0.95; Abbott PCR with artus-DSP, r = 0.97; and artus-DSP with artus-DB, r = 0.94). Bland-Altman analysis showed a good level of agreement for Abbott PCR and artus-DSP, with a mean difference of 0.10 log(10) IU/ml and limits of agreement of -0.91 to 1.11 log(10) IU/ml. No genotype-specific bias was seen in all three systems for HBV genotypes A, C, and D, which are predominant in this region. This finding illustrates that the Abbott real-time HBV and artus-DSP systems show more comparable performance than the artus-DB system, meeting the current guidelines for assays to be used in the management of hepatitis B.

HLA-A, -B and -DRB1 polymorphism in Koreans defined by sequence-based typing of 4128 cord blood units.

PubMed

Huh, J Y; Yi, D Y; Eo, S-H; Cho, H; Park, M H; Kang, M S

2013-12-01

Human leucocyte antigen (HLA) alleles and haplotypes differ significantly among different ethnic groups, and high-resolution typing methods allow for the detection of a wider spectrum of HLA variations. In this study, HLA-A, -B and -DRB1 genotypes were analysed in 4128 cord blood units obtained from Korean women using the sequence-based typing method. A total of 44 HLA-A, 67 HLA-B and 48 HLA-DRB1 most probable alleles were identified. Of these, high-frequency alleles found at a frequency of ≥5% were 6 HLA-A (A*02:01, A*02:06, A*11:01, A*24:02, A*31:01, A*33:03), 5 HLA-B (B*15:01, B*44:03, B*51:01, B*54:01, B*58:01) and 7 HLA-DRB1 (DRB1*01:01, DRB1*04:05, DRB1*07:01, DRB1*08:03, DRB1*09:01, DRB1*13:02, DRB1*15:01) alleles. At each locus, A*02, B*15 and DRB1*04 generic groups were most diverse at allelic level, consisting of 8, 11 and 10 different alleles, respectively. Two- and three-locus haplotypes estimated by the maximum likelihood method revealed 73 A-B, 74 B-DRB1 and 42 A-B-DRB1 haplotypes with frequencies of ≥0.3%. A total of 193 A-B-DRB1 haplotypes found at a frequency of ≥0.1% were presented, and the six most common haplotypes were A*33:03-B*44:03-DRB1*13:02 (4.6%), A*33:03-B*58:01-DRB1*13:02 (3.0%), A*24:02-B*07:02-DRB1*01:01 (2.7%), A*33:03-B*44:03-DRB1*07:01 (2.5%), A*30:01-B*13:02-DRB1*07:01 (2.2%) and A*24:02-B*52:01-DRB1*15:02 (2.1%). Compared with previous smaller scale studies, this study further delineated the allelic and haplotypic diversity in Koreans including low-frequency alleles and haplotypes. Information obtained in this study will be useful for the search for unrelated bone marrow donors and for anthropologic and disease association studies. © 2013 John Wiley & Sons Ltd.

The Raptor Real-Time Processing Architecture

NASA Astrophysics Data System (ADS)

Galassi, M.; Starr, D.; Wozniak, P.; Brozdin, K.

The primary goal of Raptor is ambitious: to identify interesting optical transients from very wide field of view telescopes in real time, and then to quickly point the higher resolution Raptor ``fovea'' cameras and spectrometer to the location of the optical transient. The most interesting of Raptor's many applications is the real-time search for orphan optical counterparts of Gamma Ray Bursts. The sequence of steps (data acquisition, basic calibration, source extraction, astrometry, relative photometry, the smarts of transient identification and elimination of false positives, telescope pointing feedback, etc.) is implemented with a ``component'' approach. All basic elements of the pipeline functionality have been written from scratch or adapted (as in the case of SExtractor for source extraction) to form a consistent modern API operating on memory resident images and source lists. The result is a pipeline which meets our real-time requirements and which can easily operate as a monolithic or distributed processing system. Finally, the Raptor architecture is entirely based on free software (sometimes referred to as ``open source'' software). In this paper we also discuss the interplay between various free software technologies in this type of astronomical problem.

Mapping the binding site of aflatoxin B/sub 1/ in DNA: systematic analysis of the reactivity of aflatoxin B/sub 1/ with guanines in different DNA sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benasutti, M.; Ejadi, S.; Whitlow, M.D.

The mutagenic and carcinogenic chemical aflatoxin B/sub 1/ (AFB/sub 1/) reacts almost exclusively at the N(7)-position of guanine following activation to its reactive form, the 8,9-epoxide (AFB/sub 1/ oxide). In general N(7)-guanine adducts yield DNA strand breaks when heated in base, a property that serves as the basis for the Maxam-Gilbert DNA sequencing reaction specific for guanine. Using DNA sequencing methods, other workers have shown that AFB/sub 1/ oxide gives strand breaks at positions of guanines; however, the guanine bands varied in intensity. This phenomenon has been used to infer that AFB/sub 1/ oxide prefers to react with guanines inmore » some sequence contexts more than in others and has been referred to as sequence specificity of binding. Herein, data on the reaction of AFB/sub 1/ oxide with several synthetic DNA polymers with different sequences are presented, and (following hydrolysis) adduct levels are determine by high-pressure liquid chromatography. These results reveal that for AFB/sub 1/ oxide (1) the N(7)-guanine adduct is the major adduct found in all of the DNA polymers, (2) adduct levels vary in different sequences, and, thus, sequence specificity is also observed by this more direct method, and (3) the intensity of bands in DNA sequencing gels is likely to reflect adduct levels formed at the N(7)-position of guanine. Knowing this, a reinvestigation of the reactivity of guanines in different DNA sequences using DNA sequencing methods was undertaken. Methods are developed to determine the X (5'-side) base and the Y (3'-side) base are most influential in determining guanine reactivity. These rules in conjunction with molecular modeling studies were used to assess the binding sites that might be utilized by AFB/sub 1/ oxide in its reaction with DNA.« less

Characterization of real-time computers

NASA Technical Reports Server (NTRS)

Shin, K. G.; Krishna, C. M.

1984-01-01

A real-time system consists of a computer controller and controlled processes. Despite the synergistic relationship between these two components, they have been traditionally designed and analyzed independently of and separately from each other; namely, computer controllers by computer scientists/engineers and controlled processes by control scientists. As a remedy for this problem, in this report real-time computers are characterized by performance measures based on computer controller response time that are: (1) congruent to the real-time applications, (2) able to offer an objective comparison of rival computer systems, and (3) experimentally measurable/determinable. These measures, unlike others, provide the real-time computer controller with a natural link to controlled processes. In order to demonstrate their utility and power, these measures are first determined for example controlled processes on the basis of control performance functionals. They are then used for two important real-time multiprocessor design applications - the number-power tradeoff and fault-masking and synchronization.

Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains.

PubMed

Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

2011-02-01

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536(T), M. massiliense CIP 108297(T), and M. bolletii CIP 108541(T)) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the

Multilocus Sequence Analysis and rpoB Sequencing of Mycobacterium abscessus (Sensu Lato) Strains▿

PubMed Central

Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

2011-01-01

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536T, M. massiliense CIP 108297T, and M. bolletii CIP 108541T) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering

VAXELN Experimentation: Programming a Real-Time Periodic Task Dispatcher Using VAXELN Ada 1.1

DTIC Science & Technology

1987-11-01

synchronization to the SQM and VAXELN semaphores. Based on real-time scheduling theory, the optimal rate-monotonic scheduling algorithm [Lui 73...schedulability test based on the rate-monotonic algorithm , namely task-lumping [Sha 871, was necessary to cal- culate the theoretically expected schedulability...8217 Guide Digital Equipment Corporation, Maynard, MA, 1986. [Lui 73] Liu, C.L., Layland, J.W. Scheduling Algorithms for Multi-programming in a Hard-Real-Time

Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping.

PubMed

Sridhar, Siddharth; Yip, Cyril C Y; Chan, Jasper F W; To, Kelvin K W; Cheng, Vincent C C; Yuen, Kwok-Yung

2018-05-01

The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping. Copyright © 2018 Elsevier Inc. All rights reserved.

HLA-B*5808, a new HLA-B allele characterized by sequence based typing.

PubMed

Poli, F; Crespiatico, L; Frison, S; Longhi, E; Marlianici, E; Scalamogna, M

2003-12-01

This brief communication describes a new HLA-B allele (HLA-B*5808) detected in an Italian white volunteer bone marrow donor. With serology, this subject was typed as HLA-B15,17, whereas with molecular biology B*15, B*51, B*52 and/or B*58 could be assigned. In order to clarify the results, direct and cloning sequencing of exons 2, 3 and 4 were carried out. This new allele is identical to HLA-B*5801 in exon 2 except for a silent point mutation at nucleotide 141 where a C is substituted by a T; exons 3 and 4 are typical of HLA-B*51, B*52 and B*78. The peculiar sequence of B*5808 could explain the discrepancy between the serological and molecular typing results.

Profiling of Oral Microbiota in Early Childhood Caries Using Single-Molecule Real-Time Sequencing

PubMed Central

Wang, Yuan; Zhang, Jie; Chen, Xi; Jiang, Wen; Wang, Sa; Xu, Lei; Tu, Yan; Zheng, Pei; Wang, Ying; Lin, Xiaolong; Chen, Hui

2017-01-01

Background: Alterations of oral microbiota are the main cause of the progression of caries. The goal of this study was to characterize the oral microbiota in childhood caries based on single-molecule real-time sequencing. Methods: A total of 21 preschoolers, aged 3–5 years old with severe early childhood caries, and 20 age-matched, caries-free children as controls were recruited. Saliva samples were collected, followed by DNA extraction, Pacbio sequencing, and phylogenetic analyses of the oral microbial communities. Results: Eight hundred and seventy six species derived from 13 known bacterial phyla and 110 genera were detected from 41 children using Pacbio sequencing. At the species level, 38 species, including Veillonella spp., Streptococcus spp., Prevotella spp., and Lactobacillus spp., showed higher abundance in the caries group compared to the caries-free group (p < 0.05). The core microbiota at the genus and species levels was more stable in the caries-free micro-ecological niche. At follow-up, oral examinations 6 months after sample collection, development of new dental caries was observed in 5 children (the transitional group) among the 21 caries free children. Compared with the caries-free children, in the transitional and caries groups, 6 species, which were more abundant in the caries-free group, exhibited a relatively low abundance in both the caries group and the transitional group (p < 0.05). We conclude that Abiotrophia spp., Neisseria spp., and Veillonella spp., might be associated with healthy oral microbial ecosystem. Prevotella spp., Lactobacillus spp., Dialister spp., and Filifactor spp. may be related to the pathogenesis and progression of dental caries. PMID:29187843

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

PubMed Central

Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

2015-01-01

Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity (≥ quartic time). Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm ‘sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)’, which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff’s original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. Availability and implementation: SPARSE is freely available at http://www.bioinf.uni-freiburg.de/Software/SPARSE. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25838465

Label-free thioflavin T/G-quadruplex-based real-time strand displacement amplification for biosensing applications.

PubMed

Du, Yi-Chen; Zhu, Li-Na; Kong, De-Ming

2016-12-15

To promote application of strand-displacement amplification (SDA) techniques in biosensing, a label-free, real-time monitoring strategy for isothermal nucleic acid amplification reactions was designed. G-quadruplex structures were introduced into SDA products using specific recognition of G-quadruplexes by the fluorogenic dye thioflavin T. Performance was good for real-time monitoring of traditional SDA by a linear-amplification mechanism and for exponential cross-triggered SDA amplification. The strategy worked on a commercial real-time PCR instrument, making it suitable for biosensing platforms. As examples, two highly sensitive and specific biosensors were designed for analysis of the activity of uracil-DNA glycosylase (UDG) and the restriction endonuclease EcoRI. Detection limits were 6×10(-5)U/mL for UDG and 0.016U/mL for EcoRI. Detection of corresponding targets in complex matrices such as cell lysates or human serum was also demonstrated. Compared to traditional end-point detection methods, real-time SDA-based approaches have the advantages of simple, fast operation; high sensitivity; low risk of carryover contamination; and very high throughput. The introduction of real-time monitoring strategies may promote application of SDA reactions in biosensor design. Copyright © 2016 Elsevier B.V. All rights reserved.

Agent-based real-time signal coordination in congested networks.

DOT National Transportation Integrated Search

2014-01-01

This study is the continuation of a previous NEXTRANS study on agent-based reinforcement : learning methods for signal coordination in congested networks. In the previous study, the : formulation of a real-time agent-based traffic signal control in o...

Near real-time estimation of ionosphere vertical total electron content from GNSS satellites using B-splines in a Kalman filter

NASA Astrophysics Data System (ADS)

Erdogan, Eren; Schmidt, Michael; Seitz, Florian; Durmaz, Murat

2017-02-01

Although the number of terrestrial global navigation satellite system (GNSS) receivers supported by the International GNSS Service (IGS) is rapidly growing, the worldwide rather inhomogeneously distributed observation sites do not allow the generation of high-resolution global ionosphere products. Conversely, with the regionally enormous increase in highly precise GNSS data, the demands on (near) real-time ionosphere products, necessary in many applications such as navigation, are growing very fast. Consequently, many analysis centers accepted the responsibility of generating such products. In this regard, the primary objective of our work is to develop a near real-time processing framework for the estimation of the vertical total electron content (VTEC) of the ionosphere using proper models that are capable of a global representation adapted to the real data distribution. The global VTEC representation developed in this work is based on a series expansion in terms of compactly supported B-spline functions, which allow for an appropriate handling of the heterogeneous data distribution, including data gaps. The corresponding series coefficients and additional parameters such as differential code biases of the GNSS satellites and receivers constitute the set of unknown parameters. The Kalman filter (KF), as a popular recursive estimator, allows processing of the data immediately after acquisition and paves the way of sequential (near) real-time estimation of the unknown parameters. To exploit the advantages of the chosen data representation and the estimation procedure, the B-spline model is incorporated into the KF under the consideration of necessary constraints. Based on a preprocessing strategy, the developed approach utilizes hourly batches of GPS and GLONASS observations provided by the IGS data centers with a latency of 1 h in its current realization. Two methods for validation of the results are performed, namely the self consistency analysis and a comparison

A real time genotyping PCR assay for polyomavirus BK.

PubMed

Gard, Lilli; Niesters, Hubert G M; Riezebos-Brilman, Annelies

2015-09-01

Polyomavirus BK (BKV) may cause nephropathy in renal transplant recipients and hemorrhagic cystitis in bone marrow recipients. We developed real-time PCRs (RT-PCR) to determine easily and rapidly the different BKV genotypes (BKGT) (I-IV). On the VP1 gene a duplex of RT-PCRs was developed and validated to differentiate the four main BKGT. 212 BKV positive samples (21 plasma, 191 urine) were tested with these specific PCRs. Of these 212 samples, 55 PCR results were additionally confirmed by sequencing a VP1 gene fragment (nucleotide 1630-1956). For every genotype, a highly specific, precise and internally controlled assay was developed with a limit of detection of log 3 copies per ml. In 18 (8.5%) of these samples genotyping was not successful due to a low viral load. By sequence analysis, the genotype of 46 out of 55 and 2 out of 4 samples with double infection could be confirmed. This study describes RT-PCRs for detection of the main BKGT. It proved to be rapid, cheap and sensitive compared to sequencing. Double infections can also be detected. This method will be of value to investigate the role of BKV infection in relation to the genotype. Copyright © 2015 Elsevier B.V. All rights reserved.

Free circulating nucleic acids in plasma and serum as a novel approach to the use of internal controls in real time PCR based detection.

PubMed

Karataylı, Ersin; Altunoğlu, Yasemin Çelik; Karataylı, Senem Ceren; Yurdaydın, Cihan; Bozdayı, A Mithat

2014-10-01

Internal controls (ICs), are the main components of any real-time PCR based amplification methods, which are co-purified and co-amplified with the actual target. The existence of free circulating nucleic acids in plasma and serum (CNAPS) has been known for many years. The aim of this study was to verify whether CNAPS can be used as ICs in real-time PCR based detection and quantification of DNA or RNA targets in plasma and serum samples. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a housekeeping gene, was chosen at random as CNAPS to serve as an intrinsic internal control in two different real-time PCR based quantification models in plasma and serum. Viral loads of hepatitis B virus (HBV) DNA and hepatitis delta virus (HDV) RNA were quantified as actual targets in parallel to GAPDH as IC in a total of 519 serum or plasma samples including 21 healthy controls, 202 positive chronic hepatitis delta patients, 37 chronic hepatitis C patients, 168 chronic hepatitis B patients, 52 patients with hepatocellular carcinoma, and 39 patients with non-alcoholic steatohepatitis/non-alcoholic fatty liver disease. GAPDH levels did not show significant variance in different patient groups and yielded positive signals in all 519 patients with persistent cycle threshold (CT) values 27.85±1.57 (mean±standard deviation (SD)). Reproducibility of the GAPDH amplification in HDV RNA and HBV DNA quantifications was shown with a SD value of CT ranging from 0.42 to 2.14 (mean SD; 1.18) and 0.24 to 1.75 (mean SD; 1.03), respectively. In conclusion, the freely circulating nucleic acids can clearly be used as internal controls for real-time PCR based detection and quantification of any RNA and mainly DNA targets (pathogens) in serum or plasma and this simply excludes the compulsory external addition of any IC molecules into the reaction. Copyright © 2014 Elsevier B.V. All rights reserved.

Characterization, adaptive traffic shaping, and multiplexing of real-time MPEG II video

NASA Astrophysics Data System (ADS)

Agrawal, Sanjay; Barry, Charles F.; Binnai, Vinay; Kazovsky, Leonid G.

1997-01-01

We obtain network traffic model for real-time MPEG-II encoded digital video by analyzing video stream samples from real-time encoders from NUKO Information Systems. MPEG-II sample streams include a resolution intensive movie, City of Joy, an action intensive movie, Aliens, a luminance intensive (black and white) movie, Road To Utopia, and a chrominance intensive (color) movie, Dick Tracy. From our analysis we obtain a heuristic model for the encoded video traffic which uses a 15-stage Markov process to model the I,B,P frame sequences within a group of pictures (GOP). A jointly-correlated Gaussian process is used to model the individual frame sizes. Scene change arrivals are modeled according to a gamma process. Simulations show that our MPEG-II traffic model generates, I,B,P frame sequences and frame sizes that closely match the sample MPEG-II stream traffic characteristics as they relate to latency and buffer occupancy in network queues. To achieve high multiplexing efficiency we propose a traffic shaping scheme which sets preferred 1-frame generation times among a group of encoders so as to minimize the overall variation in total offered traffic while still allowing the individual encoders to react to scene changes. Simulations show that our scheme results in multiplexing gains of up to 10% enabling us to multiplex twenty 6 Mbps MPEG-II video streams instead of 18 streams over an ATM/SONET OC3 link without latency or cell loss penalty. This scheme is due for a patent.

Real-time PCR probe optimization using design of experiments approach.

PubMed

Wadle, S; Lehnert, M; Rubenwolf, S; Zengerle, R; von Stetten, F

2016-03-01

Primer and probe sequence designs are among the most critical input factors in real-time polymerase chain reaction (PCR) assay optimization. In this study, we present the use of statistical design of experiments (DOE) approach as a general guideline for probe optimization and more specifically focus on design optimization of label-free hydrolysis probes that are designated as mediator probes (MPs), which are used in reverse transcription MP PCR (RT-MP PCR). The effect of three input factors on assay performance was investigated: distance between primer and mediator probe cleavage site; dimer stability of MP and target sequence (influenza B virus); and dimer stability of the mediator and universal reporter (UR). The results indicated that the latter dimer stability had the greatest influence on assay performance, with RT-MP PCR efficiency increased by up to 10% with changes to this input factor. With an optimal design configuration, a detection limit of 3-14 target copies/10 μl reaction could be achieved. This improved detection limit was confirmed for another UR design and for a second target sequence, human metapneumovirus, with 7-11 copies/10 μl reaction detected in an optimum case. The DOE approach for improving oligonucleotide designs for real-time PCR not only produces excellent results but may also reduce the number of experiments that need to be performed, thus reducing costs and experimental times.

Heritable heading time variation in wheat lines with the same number of Ppd-B1 gene copies.

PubMed

Ivaničová, Zuzana; Valárik, Miroslav; Pánková, Kateřina; Trávníčková, Martina; Doležel, Jaroslav; Šafář, Jan; Milec, Zbyněk

2017-01-01

The ability of plants to identify an optimal flowering time is critical for ensuring the production of viable seeds. The main environmental factors that influence the flowering time include the ambient temperature and day length. In wheat, the ability to assess the day length is controlled by photoperiod (Ppd) genes. Due to its allohexaploid nature, bread wheat carries the following three Ppd-1 genes: Ppd-A1, Ppd-B1 and Ppd-D1. While photoperiod (in)sensitivity controlled by Ppd-A1 and Ppd-D1 is mainly determined by sequence changes in the promoter region, the impact of the Ppd-B1 alleles on the heading time has been linked to changes in the copy numbers (and possibly their methylation status) and sequence changes in the promoter region. Here, we report that plants with the same number of Ppd-B1 copies may have different heading times. Differences were observed among F7 lines derived from crossing two spring hexaploid wheat varieties. Several lines carrying three copies of Ppd-B1 headed 16 days later than other plants in the population with the same number of gene copies. This effect was associated with changes in the gene expression level and methylation of the Ppd-B1 gene.

Heritable heading time variation in wheat lines with the same number of Ppd-B1 gene copies

PubMed Central

Ivaničová, Zuzana; Valárik, Miroslav; Pánková, Kateřina; Trávníčková, Martina; Doležel, Jaroslav; Šafář, Jan

2017-01-01

The ability of plants to identify an optimal flowering time is critical for ensuring the production of viable seeds. The main environmental factors that influence the flowering time include the ambient temperature and day length. In wheat, the ability to assess the day length is controlled by photoperiod (Ppd) genes. Due to its allohexaploid nature, bread wheat carries the following three Ppd-1 genes: Ppd-A1, Ppd-B1 and Ppd-D1. While photoperiod (in)sensitivity controlled by Ppd-A1 and Ppd-D1 is mainly determined by sequence changes in the promoter region, the impact of the Ppd-B1 alleles on the heading time has been linked to changes in the copy numbers (and possibly their methylation status) and sequence changes in the promoter region. Here, we report that plants with the same number of Ppd-B1 copies may have different heading times. Differences were observed among F7 lines derived from crossing two spring hexaploid wheat varieties. Several lines carrying three copies of Ppd-B1 headed 16 days later than other plants in the population with the same number of gene copies. This effect was associated with changes in the gene expression level and methylation of the Ppd-B1 gene. PMID:28846721

Modeling Interdependent and Periodic Real-World Action Sequences

PubMed Central

Kurashima, Takeshi; Althoff, Tim; Leskovec, Jure

2018-01-01

Mobile health applications, including those that track activities such as exercise, sleep, and diet, are becoming widely used. Accurately predicting human actions in the real world is essential for targeted recommendations that could improve our health and for personalization of these applications. However, making such predictions is extremely difficult due to the complexities of human behavior, which consists of a large number of potential actions that vary over time, depend on each other, and are periodic. Previous work has not jointly modeled these dynamics and has largely focused on item consumption patterns instead of broader types of behaviors such as eating, commuting or exercising. In this work, we develop a novel statistical model, called TIPAS, for Time-varying, Interdependent, and Periodic Action Sequences. Our approach is based on personalized, multivariate temporal point processes that model time-varying action propensities through a mixture of Gaussian intensities. Our model captures short-term and long-term periodic interdependencies between actions through Hawkes process-based self-excitations. We evaluate our approach on two activity logging datasets comprising 12 million real-world actions (e.g., eating, sleep, and exercise) taken by 20 thousand users over 17 months. We demonstrate that our approach allows us to make successful predictions of future user actions and their timing. Specifically, TIPAS improves predictions of actions, and their timing, over existing methods across multiple datasets by up to 156%, and up to 37%, respectively. Performance improvements are particularly large for relatively rare and periodic actions such as walking and biking, improving over baselines by up to 256%. This demonstrates that explicit modeling of dependencies and periodicities in real-world behavior enables successful predictions of future actions, with implications for modeling human behavior, app personalization, and targeting of health interventions. PMID

Development and validation of a novel hydrolysis probe real-time polymerase chain reaction for agamid adenovirus 1 in the central bearded dragon (Pogona vitticeps).

PubMed

Fredholm, Daniel V; Coleman, James K; Childress, April L; Wellehan, James F X

2015-03-01

Agamid adenovirus 1 (AgAdv-1) is a significant cause of disease in bearded dragons (Pogona sp.). Clinical manifestations of AgAdv-1 infection are variable and often nonspecific; the manifestations range from lethargy, weight loss, and inappetence, to severe enteritis, hepatitis, and sudden death. Currently, diagnosis of AgAdv-1 infection is achieved through a single published method: standard nested polymerase chain reaction (nPCR) and sequencing. Standard nPCR with sequencing provides reliable sensitivity, specificity, and validation of PCR products. However, this process is comparatively expensive, laborious, and slow. Probe hybridization, as used in a TaqMan assay, represents the best option for validating PCR products aside from the time-consuming process of sequencing. This study developed a real-time PCR (qPCR) assay using a TaqMan probe-based assay, targeting a highly conserved region of the AgAdv-1 genome. Standard curves were generated, detection results were compared with the gold standard conventional PCR and sequencing assay, and limits of detection were determined. Additionally, the qPCR assay was run on samples known to be positive for AgAdv-1 and samples known to be positive for other adenoviruses. Based on the results of these evaluations, this assay allows for a less expensive, rapid, quantitative detection of AgAdv-1 in bearded dragons. © 2015 The Author(s).

A rule-based system for real-time analysis of control systems

NASA Astrophysics Data System (ADS)

Larson, Richard R.; Millard, D. Edward

1992-10-01

An approach to automate the real-time analysis of flight critical health monitoring and system status is being developed and evaluated at the NASA Dryden Flight Research Facility. A software package was developed in-house and installed as part of the extended aircraft interrogation and display system. This design features a knowledge-base structure in the form of rules to formulate interpretation and decision logic of real-time data. This technique has been applied for ground verification and validation testing and flight testing monitoring where quick, real-time, safety-of-flight decisions can be very critical. In many cases post processing and manual analysis of flight system data are not required. The processing is described of real-time data for analysis along with the output format which features a message stack display. The development, construction, and testing of the rule-driven knowledge base, along with an application using the X-31A flight test program, are presented.

A rule-based system for real-time analysis of control systems

NASA Technical Reports Server (NTRS)

Larson, Richard R.; Millard, D. Edward

1992-01-01

An approach to automate the real-time analysis of flight critical health monitoring and system status is being developed and evaluated at the NASA Dryden Flight Research Facility. A software package was developed in-house and installed as part of the extended aircraft interrogation and display system. This design features a knowledge-base structure in the form of rules to formulate interpretation and decision logic of real-time data. This technique has been applied for ground verification and validation testing and flight testing monitoring where quick, real-time, safety-of-flight decisions can be very critical. In many cases post processing and manual analysis of flight system data are not required. The processing is described of real-time data for analysis along with the output format which features a message stack display. The development, construction, and testing of the rule-driven knowledge base, along with an application using the X-31A flight test program, are presented.

Comparison of DNA Microarray, Loop-Mediated Isothermal Amplification (LAMP) and Real-Time PCR with DNA Sequencing for Identification of Fusarium spp. Obtained from Patients with Hematologic Malignancies.

PubMed

de Souza, Marcela; Matsuzawa, Tetsuhiro; Sakai, Kanae; Muraosa, Yasunori; Lyra, Luzia; Busso-Lopes, Ariane Fidelis; Levin, Anna Sara Shafferman; Schreiber, Angélica Zaninelli; Mikami, Yuzuru; Gonoi, Tohoru; Kamei, Katsuhiko; Moretti, Maria Luiza; Trabasso, Plínio

2017-08-01

The performance of three molecular biology techniques, i.e., DNA microarray, loop-mediated isothermal amplification (LAMP), and real-time PCR were compared with DNA sequencing for properly identification of 20 isolates of Fusarium spp. obtained from blood stream as etiologic agent of invasive infections in patients with hematologic malignancies. DNA microarray, LAMP and real-time PCR identified 16 (80%) out of 20 samples as Fusarium solani species complex (FSSC) and four (20%) as Fusarium spp. The agreement among the techniques was 100%. LAMP exhibited 100% specificity, while DNA microarray, LAMP and real-time PCR showed 100% sensitivity. The three techniques had 100% agreement with DNA sequencing. Sixteen isolates were identified as FSSC by sequencing, being five Fusarium keratoplasticum, nine Fusarium petroliphilum and two Fusarium solani. On the other hand, sequencing identified four isolates as Fusarium non-solani species complex (FNSSC), being three isolates as Fusarium napiforme and one isolate as Fusarium oxysporum. Finally, LAMP proved to be faster and more accessible than DNA microarray and real-time PCR, since it does not require a thermocycler. Therefore, LAMP signalizes as emerging and promising methodology to be used in routine identification of Fusarium spp. among cases of invasive fungal infections.

Determination of the aflatoxin M1 (AFM1) from milk by direct analysis in real time - mass spectrometry (DART-MS)

USDA-ARS?s Scientific Manuscript database

Certain fungi that grow on crops can produce aflatoxins, which are highly carcinogenic. One of these, aflatoxin B1 can be metabolized by mammals to aflatoxin M1, a form that retains potent carcinogenicity and which can be excreted into milk. Direct analysis in real time (DART) ionization coupled to ...

Rapid and Sensitive Detection of Pseudomonas aeruginosa in Chlorinated Water and Aerosols targeting gyrB gene using Real-time PCR

PubMed Central

Lee, Chang Soo; Wetzel, Kaedra; Buckley, Timothy; Wozniak, Daniel; Lee, Jiyoung

2011-01-01

Aims For the rapid detection of P. aeruginosa from chlorinated water and aerosols, gyrB gene-based real-time PCR assay was developed and investigated. Methods and Results Two novel primer sets (pa722F/746MGB/899R and pa722F/746MGB/788R) were designed using the most updated 611 Pseudomonas and 748 other bacterial gyrB genes for achieving high specificity. Their specificity showed 100% accuracy when tested with various strains including clinical isolates from cystic fibrosis patients. The assay was tested with P. aeruginosa-containing chlorinated water and aerosols to simulate the waterborne and airborne transmission routes (detection limit 3.3 × 102 CFU·PCR−1 − 2.3 × 103 CFU·PCR−1). No chlorine interference in real-time PCR was observed at drinking water level (~ 1 mg·L−1), but high level of chorine (12 mg·L−1) interfered the assay, thus neutralization was needed. P. aeruginosa in aerosol was successfully detected after capturing with gelatin filters with minimum 2 min of sampling time when the initial concentration of 104 CFU·mL−1 bacteria existed in the nebulizer. Conclusions A highly specific and rapid assay (2–3 hrs) was developed by targeting gyrB gene for the detection of P. aeruginosa in chlorinated water and aerosols, combined with optimized sample collection methods and sample processing, so the direct DNA extraction from either water or aerosol was possible while achieving the desired sensitivity of the method. Significance and Impact The new assay can provide timely and accurate risk assessment to prevent P. aeruginosa exposure from water and aerosol, resulting in reduced disease burden, especially among immune-compromised and susceptible individuals. This approach can be easily utilized as a platform technology for the detection of other types of microorganisms, especially for those that are transmitted via water and aerosol routes, such as Legionella pneumophila. PMID:21794031

Software-Based Real-Time Acquisition and Processing of PET Detector Raw Data.

PubMed

Goldschmidt, Benjamin; Schug, David; Lerche, Christoph W; Salomon, André; Gebhardt, Pierre; Weissler, Bjoern; Wehner, Jakob; Dueppenbecker, Peter M; Kiessling, Fabian; Schulz, Volkmar

2016-02-01

In modern positron emission tomography (PET) readout architectures, the position and energy estimation of scintillation events (singles) and the detection of coincident events (coincidences) are typically carried out on highly integrated, programmable printed circuit boards. The implementation of advanced singles and coincidence processing (SCP) algorithms for these architectures is often limited by the strict constraints of hardware-based data processing. In this paper, we present a software-based data acquisition and processing architecture (DAPA) that offers a high degree of flexibility for advanced SCP algorithms through relaxed real-time constraints and an easily extendible data processing framework. The DAPA is designed to acquire detector raw data from independent (but synchronized) detector modules and process the data for singles and coincidences in real-time using a center-of-gravity (COG)-based, a least-squares (LS)-based, or a maximum-likelihood (ML)-based crystal position and energy estimation approach (CPEEA). To test the DAPA, we adapted it to a preclinical PET detector that outputs detector raw data from 60 independent digital silicon photomultiplier (dSiPM)-based detector stacks and evaluated it with a [(18)F]-fluorodeoxyglucose-filled hot-rod phantom. The DAPA is highly reliable with less than 0.1% of all detector raw data lost or corrupted. For high validation thresholds (37.1 ± 12.8 photons per pixel) of the dSiPM detector tiles, the DAPA is real time capable up to 55 MBq for the COG-based CPEEA, up to 31 MBq for the LS-based CPEEA, and up to 28 MBq for the ML-based CPEEA. Compared to the COG-based CPEEA, the rods in the image reconstruction of the hot-rod phantom are only slightly better separable and less blurred for the LS- and ML-based CPEEA. While the coincidence time resolution (∼ 500 ps) and energy resolution (∼12.3%) are comparable for all three CPEEA, the system sensitivity is up to 2.5 × higher for the LS- and ML-based CPEEA.

Real-Time, Sensor-Based Computing in the Laboratory.

ERIC Educational Resources Information Center

Badmus, O. O.; And Others

1996-01-01

Demonstrates the importance of Real-Time, Sensor-Based (RTSB) computing and how it can be easily and effectively integrated into university student laboratories. Describes the experimental processes, the process instrumentation and process-computer interface, the computer and communications systems, and typical software. Provides much technical…

Real-time detection of small and dim moving objects in IR video sequences using a robust background estimator and a noise-adaptive double thresholding

NASA Astrophysics Data System (ADS)

Zingoni, Andrea; Diani, Marco; Corsini, Giovanni

2016-10-01

We developed an algorithm for automatically detecting small and poorly contrasted (dim) moving objects in real-time, within video sequences acquired through a steady infrared camera. The algorithm is suitable for different situations since it is independent of the background characteristics and of changes in illumination. Unlike other solutions, small objects of any size (up to single-pixel), either hotter or colder than the background, can be successfully detected. The algorithm is based on accurately estimating the background at the pixel level and then rejecting it. A novel approach permits background estimation to be robust to changes in the scene illumination and to noise, and not to be biased by the transit of moving objects. Care was taken in avoiding computationally costly procedures, in order to ensure the real-time performance even using low-cost hardware. The algorithm was tested on a dataset of 12 video sequences acquired in different conditions, providing promising results in terms of detection rate and false alarm rate, independently of background and objects characteristics. In addition, the detection map was produced frame by frame in real-time, using cheap commercial hardware. The algorithm is particularly suitable for applications in the fields of video-surveillance and computer vision. Its reliability and speed permit it to be used also in critical situations, like in search and rescue, defence and disaster monitoring.

Advanced Hard Real-Time Operating System, the Maruti Project. Part 2.

DTIC Science & Technology

1997-01-01

Real - Time Operating System , The Maruti Project DASG-60-92-C-0055 5b. Program Element # 62301E 6. Author(s...The maruti hard real - time " operating system . A CM SIGOPS, Operating Systems Review. 23:90-106, July 1989. 254 !1 110) C. L. Liu and J. Layland...February 14, 1995 Abstract The Maruti Real - Time Operating System was developed for applications that must meet hard real-time constraints. In order

BurkDiff: a real-time PCR allelic discrimination assay for Burkholderia pseudomallei and B. mallei.

PubMed

Bowers, Jolene R; Engelthaler, David M; Ginther, Jennifer L; Pearson, Talima; Peacock, Sharon J; Tuanyok, Apichai; Wagner, David M; Currie, Bart J; Keim, Paul S

2010-11-12

A real-time PCR assay, BurkDiff, was designed to target a unique conserved region in the B. pseudomallei and B. mallei genomes containing a SNP that differentiates the two species. Sensitivity and specificity were assessed by screening BurkDiff across 469 isolates of B. pseudomallei, 49 isolates of B. mallei, and 390 isolates of clinically relevant non-target species. Concordance of results with traditional speciation methods and no cross-reactivity to non-target species show BurkDiff is a robust, highly validated assay for the detection and differentiation of B. pseudomallei and B. mallei.

Real-time simulation of thermal shadows with EMIT

NASA Astrophysics Data System (ADS)

Klein, Andreas; Oberhofer, Stefan; Schätz, Peter; Nischwitz, Alfred; Obermeier, Paul

2016-05-01

Modern missile systems use infrared imaging for tracking or target detection algorithms. The development and validation processes of these missile systems need high fidelity simulations capable of stimulating the sensors in real-time with infrared image sequences from a synthetic 3D environment. The Extensible Multispectral Image Generation Toolset (EMIT) is a modular software library developed at MBDA Germany for the generation of physics-based infrared images in real-time. EMIT is able to render radiance images in full 32-bit floating point precision using state of the art computer graphics cards and advanced shader programs. An important functionality of an infrared image generation toolset is the simulation of thermal shadows as these may cause matching errors in tracking algorithms. However, for real-time simulations, such as hardware in the loop simulations (HWIL) of infrared seekers, thermal shadows are often neglected or precomputed as they require a thermal balance calculation in four-dimensions (3D geometry in one-dimensional time up to several hours in the past). In this paper we will show the novel real-time thermal simulation of EMIT. Our thermal simulation is capable of simulating thermal effects in real-time environments, such as thermal shadows resulting from the occlusion of direct and indirect irradiance. We conclude our paper with the practical use of EMIT in a missile HWIL simulation.

Real-time synchronization of wireless sensor network by 1-PPS signal

NASA Astrophysics Data System (ADS)

Giammarini, Marco; Pieralisi, Marco; Isidori, Daniela; Concettoni, Enrico; Cristalli, Cristina; Fioravanti, Matteo

2015-05-01

The use of wireless sensor networks with different nodes is desirable in a smart environment, because the network setting up and installation on preexisting structures can be done without a fixed cabled infrastructure. The flexibility of the monitoring system is fundamental where the use of a considerable quantity of cables could compromise the normal exercise, could affect the quality of acquired signal and finally increase the cost of the materials and installation. The network is composed of several intelligent "nodes", which acquires data from different kind of sensors, and then store or transmit them to a central elaboration unit. The synchronization of data acquisition is the core of the real-time wireless sensor network (WSN). In this paper, we present a comparison between different methods proposed by literature for the real-time acquisition in a WSN and finally we present our solution based on 1-Pulse-Per-Second (1-PPS) signal generated by GPS systems. The sensor node developed is a small-embedded system based on ARM microcontroller that manages the acquisition, the timing and the post-processing of the data. The communications between the sensors and the master based on IEEE 802.15.4 protocol and managed by dedicated software. Finally, we present the preliminary results obtained on a 3 floor building simulator with the wireless sensors system developed.

Statistical tools for transgene copy number estimation based on real-time PCR.

PubMed

Yuan, Joshua S; Burris, Jason; Stewart, Nathan R; Mentewab, Ayalew; Stewart, C Neal

2007-11-01

As compared with traditional transgene copy number detection technologies such as Southern blot analysis, real-time PCR provides a fast, inexpensive and high-throughput alternative. However, the real-time PCR based transgene copy number estimation tends to be ambiguous and subjective stemming from the lack of proper statistical analysis and data quality control to render a reliable estimation of copy number with a prediction value. Despite the recent progresses in statistical analysis of real-time PCR, few publications have integrated these advancements in real-time PCR based transgene copy number determination. Three experimental designs and four data quality control integrated statistical models are presented. For the first method, external calibration curves are established for the transgene based on serially-diluted templates. The Ct number from a control transgenic event and putative transgenic event are compared to derive the transgene copy number or zygosity estimation. Simple linear regression and two group T-test procedures were combined to model the data from this design. For the second experimental design, standard curves were generated for both an internal reference gene and the transgene, and the copy number of transgene was compared with that of internal reference gene. Multiple regression models and ANOVA models can be employed to analyze the data and perform quality control for this approach. In the third experimental design, transgene copy number is compared with reference gene without a standard curve, but rather, is based directly on fluorescence data. Two different multiple regression models were proposed to analyze the data based on two different approaches of amplification efficiency integration. Our results highlight the importance of proper statistical treatment and quality control integration in real-time PCR-based transgene copy number determination. These statistical methods allow the real-time PCR-based transgene copy number estimation

Real-time simulation of a Doubly-Fed Induction Generator based wind power system on eMEGASimRTM Real-Time Digital Simulator

NASA Astrophysics Data System (ADS)

Boakye-Boateng, Nasir Abdulai

The growing demand for wind power integration into the generation mix prompts the need to subject these systems to stringent performance requirements. This study sought to identify the required tools and procedures needed to perform real-time simulation studies of Doubly-Fed Induction Generator (DFIG) based wind generation systems as basis for performing more practical tests of reliability and performance for both grid-connected and islanded wind generation systems. The author focused on developing a platform for wind generation studies and in addition, the author tested the performance of two DFIG models on the platform real-time simulation model; an average SimpowerSystemsRTM DFIG wind turbine, and a detailed DFIG based wind turbine using ARTEMiSRTM components. The platform model implemented here consists of a high voltage transmission system with four integrated wind farm models consisting in total of 65 DFIG based wind turbines and it was developed and tested on OPAL-RT's eMEGASimRTM Real-Time Digital Simulator.

A system for real-time measurement of the brachial artery diameter in B-mode ultrasound images.

PubMed

Gemignani, Vincenzo; Faita, Francesco; Ghiadoni, Lorenzo; Poggianti, Elisa; Demi, Marcello

2007-03-01

The measurement of the brachial artery diameter is frequently used in clinical studies for evaluating the flow-mediated dilation and, in conjunction with the blood pressure value, for assessing arterial stiffness. This paper presents a system for computing the brachial artery diameter in real-time by analyzing B-mode ultrasound images. The method is based on a robust edge detection algorithm which is used to automatically locate the two walls of the vessel. The measure of the diameter is obtained with subpixel precision and with a temporal resolution of 25 samples/s, so that the small dilations induced by the cardiac cycle can also be retrieved. The algorithm is implemented on a standalone video processing board which acquires the analog video signal from the ultrasound equipment. Results are shown in real-time on a graphical user interface. The system was tested both on synthetic ultrasound images and in clinical studies of flow-mediated dilation. Accuracy, robustness, and intra/inter observer variability of the method were evaluated.

Lessons Learned from Real-Time, Event-Based Internet Science Communications

NASA Technical Reports Server (NTRS)

Phillips, T.; Myszka, E.; Gallagher, D. L.; Adams, M. L.; Koczor, R. J.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

For the last several years the Science Directorate at Marshall Space Flight Center has carried out a diverse program of Internet-based science communication. The Directorate's Science Roundtable includes active researchers, NASA public relations, educators, and administrators. The Science@NASA award-winning family of Web sites features science, mathematics, and space news. The program includes extended stories about NASA science, a curriculum resource for teachers tied to national education standards, on-line activities for students, and webcasts of real-time events. The focus of sharing science activities in real-time has been to involve and excite students and the public about science. Events have involved meteor showers, solar eclipses, natural very low frequency radio emissions, and amateur balloon flights. In some cases, broadcasts accommodate active feedback and questions from Internet participants. Through these projects a pattern has emerged in the level of interest or popularity with the public. The pattern differentiates projects that include science from those that do not, All real-time, event-based Internet activities have captured public interest at a level not achieved through science stories or educator resource material exclusively. The worst event-based activity attracted more interest than the best written science story. One truly rewarding lesson learned through these projects is that the public recognizes the importance and excitement of being part of scientific discovery. Flying a camera to 100,000 feet altitude isn't as interesting to the public as searching for viable life-forms at these oxygen-poor altitudes. The details of these real-time, event-based projects and lessons learned will be discussed.

Vehicle counting system using real-time video processing

NASA Astrophysics Data System (ADS)

Crisóstomo-Romero, Pedro M.

2006-02-01

Transit studies are important for planning a road network with optimal vehicular flow. A vehicular count is essential. This article presents a vehicle counting system based on video processing. An advantage of such system is the greater detail than is possible to obtain, like shape, size and speed of vehicles. The system uses a video camera placed above the street to image transit in real-time. The video camera must be placed at least 6 meters above the street level to achieve proper acquisition quality. Fast image processing algorithms and small image dimensions are used to allow real-time processing. Digital filters, mathematical morphology, segmentation and other techniques allow identifying and counting all vehicles in the image sequences. The system was implemented under Linux in a 1.8 GHz Pentium 4 computer. A successful count was obtained with frame rates of 15 frames per second for images of size 240x180 pixels and 24 frames per second for images of size 180x120 pixels, thus being able to count vehicles whose speeds do not exceed 150 km/h.

Rapid diagnosis of sepsis with TaqMan-Based multiplex real-time PCR.

PubMed

Liu, Chang-Feng; Shi, Xin-Ping; Chen, Yun; Jin, Ye; Zhang, Bing

2018-02-01

The survival rate of septic patients mainly depends on a rapid and reliable diagnosis. A rapid, broad range, specific and sensitive quantitative diagnostic test is the urgent need. Thus, we developed a TaqMan-Based Multiplex real-time PCR assays to identify bloodstream pathogens within a few hours. Primers and TaqMan probes were designed to be complementary to conserved regions in the 16S rDNA gene of different kinds of bacteria. To evaluate accurately, sensitively, and specifically, the known bacteria samples (Standard strains, whole blood samples) are determined by TaqMan-Based Multiplex real-time PCR. In addition, 30 blood samples taken from patients with clinical symptoms of sepsis were tested by TaqMan-Based Multiplex real-time PCR and blood culture. The mean frequency of positive for Multiplex real-time PCR was 96% at a concentration of 100 CFU/mL, and it was 100% at a concentration greater than 1000 CFU/mL. All the known blood samples and Standard strains were detected positively by TaqMan-Based Multiplex PCR, no PCR products were detected when DNAs from other bacterium were used in the multiplex assay. Among the 30 patients with clinical symptoms of sepsis, 18 patients were confirmed positive by Multiplex real-time PCR and seven patients were confirmed positive by blood culture. TaqMan-Based Multiplex real-time PCR assay with highly sensitivity, specificity and broad detection range, is a rapid and accurate method in the detection of bacterial pathogens of sepsis and should have a promising usage in the diagnosis of sepsis. © 2017 Wiley Periodicals, Inc.

Distribution Locational Real-Time Pricing Based Smart Building Control and Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hao, Jun; Dai, Xiaoxiao; Zhang, Yingchen

This paper proposes an real-virtual parallel computing scheme for smart building operations aiming at augmenting overall social welfare. The University of Denver's campus power grid and Ritchie fitness center is used for demonstrating the proposed approach. An artificial virtual system is built in parallel to the real physical system to evaluate the overall social cost of the building operation based on the social science based working productivity model, numerical experiment based building energy consumption model and the power system based real-time pricing mechanism. Through interactive feedback exchanged between the real and virtual system, enlarged social welfare, including monetary cost reductionmore » and energy saving, as well as working productivity improvements, can be achieved.« less

Dependable Real-Time Systems

DTIC Science & Technology

1991-09-30

0196 or 413 545-0720 PI E-mail Address: krithi@nirvan.cs.umass.edu, stankovic(ocs.umass.edu Grant or Contract Title: Dependable Real - Time Systems Grant...Dependable Real - Time Systems " Grant or Contract Number: N00014-85-k-0398 L " Reporting Period: 1 Oct 87 - 30 Sep 91 , 2. Summary of Accomplishments ’ 2.1 Our...in developing a sound approach to scheduling tasks in complex real - time systems , (2) developed a real-time operating system kernel, a preliminary

Performance Characteristics and Comparison of Abbott and artus Real-Time Systems for Hepatitis B Virus DNA Quantification ▿

PubMed Central

Ismail, Ashrafali M.; Sivakumar, Jayashree; Anantharam, Raghavendran; Dayalan, Sujitha; Samuel, Prasanna; Fletcher, Gnanadurai J.; Gnanamony, Manu; Abraham, Priya

2011-01-01

Virological monitoring of hepatitis B virus (HBV) DNA is critical to the management of HBV infection. With several HBV DNA quantification assays available, it is important to use the most efficient testing system for virological monitoring. In this study, we evaluated the performance characteristics and comparability of three HBV DNA quantification systems: Abbott HBV real-time PCR (Abbott PCR), artus HBV real-time PCR with QIAamp DNA blood kit purification (artus-DB), and artus HBV real-time PCR with the QIAamp DSP virus kit purification (artus-DSP). The lower limits of detection of these systems were established against the WHO international standards for HBV DNA and were found to be 1.43, 82, and 9 IU/ml, respectively. The intra-assay and interassay coefficients of variation of plasma samples (1 to 6 log10 IU/ml) ranged between 0.05 to 8.34% and 0.16 to 3.48% for the Abbott PCR, 1.53 to 26.85% and 0.50 to 12.89% for artus-DB, and 0.29 to 7.42% and 0.94 to 3.01% for artus-DSP, respectively. Ninety HBV clinical samples were used for comparison of assays, and paired quantitative results showed strong correlation by linear regression analysis (artus-DB with Abbott PCR, r = 0.95; Abbott PCR with artus-DSP, r = 0.97; and artus-DSP with artus-DB, r = 0.94). Bland-Altman analysis showed a good level of agreement for Abbott PCR and artus-DSP, with a mean difference of 0.10 log10 IU/ml and limits of agreement of −0.91 to 1.11 log10 IU/ml. No genotype-specific bias was seen in all three systems for HBV genotypes A, C, and D, which are predominant in this region. This finding illustrates that the Abbott real-time HBV and artus-DSP systems show more comparable performance than the artus-DB system, meeting the current guidelines for assays to be used in the management of hepatitis B. PMID:21795507

Beyond DNA Sequencing in Space: Current and Future Omics Capabilities of the Biomolecule Sequencer Payload

NASA Technical Reports Server (NTRS)

Wallace, Sarah

2017-01-01

Why do we need a DNA sequencer to support the human exploration of space? (A) Operational environmental monitoring; (1) Identification of contaminating microbes, (2) Infectious disease diagnosis, (3) Reduce down mass (sample return for environmental monitoring, crew health, etc.). (B) Research; (1) Human, (2) Animal, (3) Microbes/Cell lines, (4) Plant. (C) Med Ops; (1) Response to countermeasures, (2) Radiation, (3) Real-time analysis can influence medical intervention. (C) Support astrobiology science investigations; (1) Technology superiorly suited to in situ nucleic acid-based life detection, (2) Functional testing for integration into robotics for extraplanetary exploration mission.

A VLSI chip set for real time vector quantization of image sequences

NASA Technical Reports Server (NTRS)

Baker, Richard L.

1989-01-01

The architecture and implementation of a VLSI chip set that vector quantizes (VQ) image sequences in real time is described. The chip set forms a programmable Single-Instruction, Multiple-Data (SIMD) machine which can implement various vector quantization encoding structures. Its VQ codebook may contain unlimited number of codevectors, N, having dimension up to K = 64. Under a weighted least squared error criterion, the engine locates at video rates the best code vector in full-searched or large tree searched VQ codebooks. The ability to manipulate tree structured codebooks, coupled with parallelism and pipelining, permits searches in as short as O (log N) cycles. A full codebook search results in O(N) performance, compared to O(KN) for a Single-Instruction, Single-Data (SISD) machine. With this VLSI chip set, an entire video code can be built on a single board that permits realtime experimentation with very large codebooks.

St. Patrick's Day 2015 geomagnetic storm analysis based on Real Time Ionosphere Monitoring

NASA Astrophysics Data System (ADS)

García-Rigo, Alberto

2017-04-01

Ionosphere Monitoring (RTIM) is a new Working Group within the International Association of Geodesy (IAG) Sub-Commission 4.3 "Atmosphere Remote Sensing". The complementary expertise of the participating research groups allows to analyse the ionospheric behaviour from a broad perspective, taking benefit of comparing multiple independent real time and near real time ionospheric approaches. In this context, a detailed analysis will be presented for the days in March, 2015 surrounding St. Patrick's Day 2015 geomagnetic storm, based on the existing ionospheric models (global or regional) within the group, which are mainly based on Global Navigation Satellite Systems (GNSS) and ionosonde data. For this purpose, a variety of ionospheric parameters will be considered, including Total Electron Content (TEC), F2 layer critical frequency (foF2), F2 layer peak (hmF2), bottomside half-thickness (B0) and ionospheric disturbance W-index. Also, ionospheric high-frequency perturbations such as Travelling Ionospheric Disturbances (TIDs), scintillations and the impact of solar flares facing the Earth will be presented to derive a clear picture of the ionospheric dynamics. Among other sources of information to take part in the comparisons, there will be (1) scintillation results -from MONITOR ESA/ESTEC-funded project- derived by means of S4 index and Sigma Phi (IEEA), specially significant in the African sector and European high latitudes, (2) dynamics of the global maps of W-index with 1h resolution derived from JPL Global Ionospheric Maps (GIMs; IZMIRAN), (3) deviations from expected quiet-time behavior analysed in terms of foF2, hmF2, B0 and B1 based on IRTAM and GIRO network of digisondes (Lowell), showing F2 layer peculiar changes due to the storm, (4) statistics based on the median of the VTEC for the 15 previous days considering VTEC european regional maps (ROB), (5) time series of VTEC data that are derived by running the NRT ionosphere model of DGFI-TUM in offline mode, which show

Real-time notification and improved situational awareness in fire emergencies using geospatial-based publish/subscribe

NASA Astrophysics Data System (ADS)

Kassab, Ala'; Liang, Steve; Gao, Yang

2010-12-01

Emergency agencies seek to maintain situational awareness and effective decision making through continuous monitoring of, and real-time alerting about, sources of information regarding current incidents and developing fire hazards. The nature of this goal requires integrating different, potentially numerous, sources of dynamic geospatial information on the one side, and a large number of clients having heterogeneous and specific interests in data on the other side. In such scenarios, the traditional request/reply communication style may function inefficiently, as it is based on point-to-point, synchronous, and pulling mode interaction between consumer clients and information providers/services. In this work, we propose Geospatial-based Publish/ Subscribe, an interaction framework that serves as a middleware for real-time transacting of spatially related information of interest, termed geospatial events, in distributed systems. Expressive data models, including geospatial event and geospatial subscription, as well as an efficient matching approach for fast dissemination of geospatial events to interested clients, are introduced. The proposed interaction framework is realized through the development of a Real-Time Fire Emergency Response System (RFERS) prototype. The prototype is designed for transacting several topics of geospatial events that are crucial within the context of fire emergencies, including GPS locations of emergency assets, meteorological observations of wireless sensors, fire incidents reports, and temporal sequences of remote sensing images of active wildfires. The performance of the system prototype has been evaluated in order to demonstrate its efficiency.

Biosensor-based real-time monitoring of paracetamol photocatalytic degradation.

PubMed

Calas-Blanchard, Carole; Istamboulié, Georges; Bontoux, Margot; Plantard, Gaël; Goetz, Vincent; Noguer, Thierry

2015-07-01

This paper presents for the first time the integration of a biosensor for the on-line, real-time monitoring of a photocatalytic degradation process. Paracetamol was used as a model molecule due to its wide use and occurrence in environmental waters. The biosensor was developed based on tyrosinase immobilization in a polyvinylalcohol photocrosslinkable polymer. It was inserted in a computer-controlled flow system installed besides a photocatalytic reactor including titanium dioxide (TiO2) as photocatalyst. It was shown that the biosensor was able to accurately monitor the paracetamol degradation with time. Compared with conventional HPLC analysis, the described device provides a real-time information on the reaction advancement, allowing a better control of the photodegradation process. Copyright © 2015 Elsevier Ltd. All rights reserved.

Digital Sequences and a Time Reversal-Based Impact Region Imaging and Localization Method

PubMed Central

Qiu, Lei; Yuan, Shenfang; Mei, Hanfei; Qian, Weifeng

2013-01-01

To reduce time and cost of damage inspection, on-line impact monitoring of aircraft composite structures is needed. A digital monitor based on an array of piezoelectric transducers (PZTs) is developed to record the impact region of impacts on-line. It is small in size, lightweight and has low power consumption, but there are two problems with the impact alarm region localization method of the digital monitor at the current stage. The first one is that the accuracy rate of the impact alarm region localization is low, especially on complex composite structures. The second problem is that the area of impact alarm region is large when a large scale structure is monitored and the number of PZTs is limited which increases the time and cost of damage inspections. To solve the two problems, an impact alarm region imaging and localization method based on digital sequences and time reversal is proposed. In this method, the frequency band of impact response signals is estimated based on the digital sequences first. Then, characteristic signals of impact response signals are constructed by sinusoidal modulation signals. Finally, the phase synthesis time reversal impact imaging method is adopted to obtain the impact region image. Depending on the image, an error ellipse is generated to give out the final impact alarm region. A validation experiment is implemented on a complex composite wing box of a real aircraft. The validation results show that the accuracy rate of impact alarm region localization is approximately 100%. The area of impact alarm region can be reduced and the number of PZTs needed to cover the same impact monitoring region is reduced by more than a half. PMID:24084123

Real-time plasma control based on the ISTTOK tomography diagnostica)

NASA Astrophysics Data System (ADS)

Carvalho, P. J.; Carvalho, B. B.; Neto, A.; Coelho, R.; Fernandes, H.; Sousa, J.; Varandas, C.; Chávez-Alarcón, E.; Herrera-Velázquez, J. J. E.

2008-10-01

The presently available processing power in generic processing units (GPUs) combined with state-of-the-art programmable logic devices benefits the implementation of complex, real-time driven, data processing algorithms for plasma diagnostics. A tomographic reconstruction diagnostic has been developed for the ISTTOK tokamak, based on three linear pinhole cameras each with ten lines of sight. The plasma emissivity in a poloidal cross section is computed locally on a submillisecond time scale, using a Fourier-Bessel algorithm, allowing the use of the output signals for active plasma position control. The data acquisition and reconstruction (DAR) system is based on ATCA technology and consists of one acquisition board with integrated field programmable gate array (FPGA) capabilities and a dual-core Pentium module running real-time application interface (RTAI) Linux. In this paper, the DAR real-time firmware/software implementation is presented, based on (i) front-end digital processing in the FPGA; (ii) a device driver specially developed for the board which enables streaming data acquisition to the host GPU; and (iii) a fast reconstruction algorithm running in Linux RTAI. This system behaves as a module of the central ISTTOK control and data acquisition system (FIRESIGNAL). Preliminary results of the above experimental setup are presented and a performance benchmarking against the magnetic coil diagnostic is shown.

CD-SEM real time bias correction using reference metrology based modeling

NASA Astrophysics Data System (ADS)

Ukraintsev, V.; Banke, W.; Zagorodnev, G.; Archie, C.; Rana, N.; Pavlovsky, V.; Smirnov, V.; Briginas, I.; Katnani, A.; Vaid, A.

2018-03-01

Accuracy of patterning impacts yield, IC performance and technology time to market. Accuracy of patterning relies on optical proximity correction (OPC) models built using CD-SEM inputs and intra die critical dimension (CD) control based on CD-SEM. Sub-nanometer measurement uncertainty (MU) of CD-SEM is required for current technologies. Reported design and process related bias variation of CD-SEM is in the range of several nanometers. Reference metrology and numerical modeling are used to correct SEM. Both methods are slow to be used for real time bias correction. We report on real time CD-SEM bias correction using empirical models based on reference metrology (RM) data. Significant amount of currently untapped information (sidewall angle, corner rounding, etc.) is obtainable from SEM waveforms. Using additional RM information provided for specific technology (design rules, materials, processes) CD extraction algorithms can be pre-built and then used in real time for accurate CD extraction from regular CD-SEM images. The art and challenge of SEM modeling is in finding robust correlation between SEM waveform features and bias of CD-SEM as well as in minimizing RM inputs needed to create accurate (within the design and process space) model. The new approach was applied to improve CD-SEM accuracy of 45 nm GATE and 32 nm MET1 OPC 1D models. In both cases MU of the state of the art CD-SEM has been improved by 3x and reduced to a nanometer level. Similar approach can be applied to 2D (end of line, contours, etc.) and 3D (sidewall angle, corner rounding, etc.) cases.

Raptor -- Mining the Sky in Real Time

NASA Astrophysics Data System (ADS)

Galassi, M.; Borozdin, K.; Casperson, D.; McGowan, K.; Starr, D.; White, R.; Wozniak, P.; Wren, J.

2004-06-01

The primary goal of Raptor is ambitious: to identify interesting optical transients from very wide field of view telescopes in real time, and then to quickly point the higher resolution Raptor ``fovea'' cameras and spectrometer to the location of the optical transient. The most interesting of Raptor's many applications is the real-time search for orphan optical counterparts of Gamma Ray Bursts. The sequence of steps (data acquisition, basic calibration, source extraction, astrometry, relative photometry, the smarts of transient identification and elimination of false positives, telescope pointing feedback...) is implemented with a ``component'' aproach. All basic elements of the pipeline functionality have been written from scratch or adapted (as in the case of SExtractor for source extraction) to form a consistent modern API operating on memory resident images and source lists. The result is a pipeline which meets our real-time requirements and which can easily operate as a monolithic or distributed processing system. Finally: the Raptor architecture is entirely based on free software (sometimes referred to as "open source" software). In this paper we also discuss the interplay between various free software technologies in this type of astronomical problem.

Flanking sequence determination and event-specific detection of genetically modified wheat B73-6-1.

PubMed

Xu, Junyi; Cao, Jijuan; Cao, Dongmei; Zhao, Tongtong; Huang, Xin; Zhang, Piqiao; Luan, Fengxia

2013-05-01

In order to establish a specific identification method for genetically modified (GM) wheat, exogenous insert DNA and flanking sequence between exogenous fragment and recombinant chromosome of GM wheat B73-6-1 were successfully acquired by means of conventional polymerase chain reaction (PCR) and thermal asymmetric interlaced (TAIL)-PCR strategies. Newly acquired exogenous fragment covered the full-length sequence of transformed genes such as transformed plasmid and corresponding functional genes including marker uidA, herbicide-resistant bar, ubiquitin promoter, and high-molecular-weight gluten subunit. The flanking sequence between insert DNA revealed high similarity with Triticum turgidum A gene (GenBank: AY494981.1). A specific PCR detection method for GM wheat B73-6-1 was established on the basis of primers designed according to the flanking sequence. This specific PCR method was validated by GM wheat, GM corn, GM soybean, GM rice, and non-GM wheat. The specifically amplified target band was observed only in GM wheat B73-6-1. This method is of high specificity, high reproducibility, rapid identification, and excellent accuracy for the identification of GM wheat B73-6-1.

Seven Novel Probe Systems for Real-Time PCR Provide Absolute Single-Base Discrimination, Higher Signaling, and Generic Components

PubMed Central

Murray, James L.; Hu, Peixu; Shafer, David A.

2015-01-01

We have developed novel probe systems for real-time PCR that provide higher specificity, greater sensitivity, and lower cost relative to dual-labeled probes. The seven DNA Detection Switch (DDS)-probe systems reported here employ two interacting polynucleotide components: a fluorescently labeled probe and a quencher antiprobe. High-fidelity detection is achieved with three DDS designs: two internal probes (internal DDS and Flip probes) and a primer probe (ZIPR probe), wherein each probe is combined with a carefully engineered, slightly mismatched, error-checking antiprobe. The antiprobe blocks off-target detection over a wide range of temperatures and facilitates multiplexing. Other designs (Universal probe, Half-Universal probe, and MacMan probe) use generic components that enable low-cost detection. Finally, single-molecule G-Force probes employ guanine-mediated fluorescent quenching by forming a hairpin between adjacent C-rich and G-rich sequences. Examples provided show how these probe technologies discriminate drug-resistant Mycobacterium tuberculosis mutants, Escherichia coli O157:H7, oncogenic EGFR deletion mutations, hepatitis B virus, influenza A/B strains, and single-nucleotide polymorphisms in the human VKORC1 gene. PMID:25307756

Real-time probabilistic covariance tracking with efficient model update.

PubMed

Wu, Yi; Cheng, Jian; Wang, Jinqiao; Lu, Hanqing; Wang, Jun; Ling, Haibin; Blasch, Erik; Bai, Li

2012-05-01

The recently proposed covariance region descriptor has been proven robust and versatile for a modest computational cost. The covariance matrix enables efficient fusion of different types of features, where the spatial and statistical properties, as well as their correlation, are characterized. The similarity between two covariance descriptors is measured on Riemannian manifolds. Based on the same metric but with a probabilistic framework, we propose a novel tracking approach on Riemannian manifolds with a novel incremental covariance tensor learning (ICTL). To address the appearance variations, ICTL incrementally learns a low-dimensional covariance tensor representation and efficiently adapts online to appearance changes of the target with only O(1) computational complexity, resulting in a real-time performance. The covariance-based representation and the ICTL are then combined with the particle filter framework to allow better handling of background clutter, as well as the temporary occlusions. We test the proposed probabilistic ICTL tracker on numerous benchmark sequences involving different types of challenges including occlusions and variations in illumination, scale, and pose. The proposed approach demonstrates excellent real-time performance, both qualitatively and quantitatively, in comparison with several previously proposed trackers.

Application of the SYBR Green real-time HRM PCR technique in the differentiation of the Babesia canis canis protozoa isolated in the areas of eastern Poland.

PubMed

Adaszek, Lukasz; Winiarczyk, Stanisław

2010-04-01

The aim of this study was to determine the usefulness of the real-time polymerised chain reaction (PCR) high-resolution melting (HRM) method in the differentiation of the Babesia canis canis protozoa isolated from dogs in the areas of eastern Poland. The studies involved 20 isolates of B. canis canis qualified depending on the analysis of the 18S RNA gene sequence to group A (EU 622792) and 20 isolates qualified to group B (EU 622793). It was proven with the real-time PCR technique that the melting temperature (Tm) of the obtained products of amplification was 78 degrees C for the representatives of group A and 81 degrees C for the representatives of group B, which proves that the real-time SYBR Green HRM PCR method is a technique allowing for the differentiation of the B. canis isolates which are slightly different with respect to the genetic structure, without the necessity to carry out time-consuming studies, i.e., sequencing and restriction fragment length polymorphism.

Real-time forecasting of an epidemic using a discrete time stochastic model: a case study of pandemic influenza (H1N1-2009).

PubMed

Nishiura, Hiroshi

2011-02-16

Real-time forecasting of epidemics, especially those based on a likelihood-based approach, is understudied. This study aimed to develop a simple method that can be used for the real-time epidemic forecasting. A discrete time stochastic model, accounting for demographic stochasticity and conditional measurement, was developed and applied as a case study to the weekly incidence of pandemic influenza (H1N1-2009) in Japan. By imposing a branching process approximation and by assuming the linear growth of cases within each reporting interval, the epidemic curve is predicted using only two parameters. The uncertainty bounds of the forecasts are computed using chains of conditional offspring distributions. The quality of the forecasts made before the epidemic peak appears largely to depend on obtaining valid parameter estimates. The forecasts of both weekly incidence and final epidemic size greatly improved at and after the epidemic peak with all the observed data points falling within the uncertainty bounds. Real-time forecasting using the discrete time stochastic model with its simple computation of the uncertainty bounds was successful. Because of the simplistic model structure, the proposed model has the potential to additionally account for various types of heterogeneity, time-dependent transmission dynamics and epidemiological details. The impact of such complexities on forecasting should be explored when the data become available as part of the disease surveillance.

Real-time forecasting of an epidemic using a discrete time stochastic model: a case study of pandemic influenza (H1N1-2009)

PubMed Central

2011-01-01

Background Real-time forecasting of epidemics, especially those based on a likelihood-based approach, is understudied. This study aimed to develop a simple method that can be used for the real-time epidemic forecasting. Methods A discrete time stochastic model, accounting for demographic stochasticity and conditional measurement, was developed and applied as a case study to the weekly incidence of pandemic influenza (H1N1-2009) in Japan. By imposing a branching process approximation and by assuming the linear growth of cases within each reporting interval, the epidemic curve is predicted using only two parameters. The uncertainty bounds of the forecasts are computed using chains of conditional offspring distributions. Results The quality of the forecasts made before the epidemic peak appears largely to depend on obtaining valid parameter estimates. The forecasts of both weekly incidence and final epidemic size greatly improved at and after the epidemic peak with all the observed data points falling within the uncertainty bounds. Conclusions Real-time forecasting using the discrete time stochastic model with its simple computation of the uncertainty bounds was successful. Because of the simplistic model structure, the proposed model has the potential to additionally account for various types of heterogeneity, time-dependent transmission dynamics and epidemiological details. The impact of such complexities on forecasting should be explored when the data become available as part of the disease surveillance. PMID:21324153

Dynamic, physical-based landslide susceptibility modelling based on real-time weather data

NASA Astrophysics Data System (ADS)

Canli, Ekrem; Glade, Thomas

2016-04-01

By now there seem to be a broad consensus that due to human-induced global change the frequency and magnitude of precipitation intensities within extensive rainstorm events is expected to increase in certain parts of the world. Given the fact, that rainfall serves as one of the most common triggers for landslide initiation, also an increased landside activity might be expected. Landslide occurrence is a globally spread phenomenon that clearly needs to be handled by a variety of concepts, methods, and models. However, most of the research done with respect to landslides deals with retrospect cases, thus classical back-analysis approaches do not incorporate real-time data. This is remarkable, as most destructive landslides are related to immediate events due to external triggering factors. Only few works so far addressed real-time dynamic components for spatial landslide susceptibility and hazard assessment. Here we present an approach for integrating real-time web-based rainfall data from different sources into an automated workflow. Rain gauge measurements are interpolated into a continuous raster which in return is directly utilized in a dynamic, physical-based model. We use the Transient Rainfall Infiltration and Grid-Based Regional Slope-Stability Analysis (TRIGRS) model that was modified in a way that it is automatically updated with the most recent rainfall raster for producing hourly landslide susceptibility maps on a regional scale. To account for the uncertainties involved in spatial modelling, the model was further adjusted by not only applying single values for given geotechnical parameters, but ranges instead. The values are determined randomly between user-defined thresholds defining the parameter ranges. Consequently, a slope failure probability from a larger number of model runs is computed rather than just the distributed factor of safety. This will ultimately allow a near-real time spatial landslide alert for a given region.

Real-time target tracking of soft tissues in 3D ultrasound images based on robust visual information and mechanical simulation.

PubMed

Royer, Lucas; Krupa, Alexandre; Dardenne, Guillaume; Le Bras, Anthony; Marchand, Eric; Marchal, Maud

2017-01-01

In this paper, we present a real-time approach that allows tracking deformable structures in 3D ultrasound sequences. Our method consists in obtaining the target displacements by combining robust dense motion estimation and mechanical model simulation. We perform evaluation of our method through simulated data, phantom data, and real-data. Results demonstrate that this novel approach has the advantage of providing correct motion estimation regarding different ultrasound shortcomings including speckle noise, large shadows and ultrasound gain variation. Furthermore, we show the good performance of our method with respect to state-of-the-art techniques by testing on the 3D databases provided by MICCAI CLUST'14 and CLUST'15 challenges. Copyright © 2016 Elsevier B.V. All rights reserved.

A novel HLA-B allele, B*5214, detected in a Taiwanese volunteer bone marrow donor using a sequence-based typing method.

PubMed

Chen, M J; Chu, C C; Shyr, M H; Lin, C L; Lin, P Y; Yang, K L

2010-02-01

HLA-B*5214, a novel rare allele of HLA-B*52 variant, was found in a Taiwanese volunteer bone marrow donor by sequence-based typing method. The sequence of B*5214 is identical to that of B*520101 in exon 2 but differs from B*520101 in exon 3 at nucleotide positions 419 A-->T and 435 A-->G. Alteration of these two nucleotides resulted an amino acid substitution at amino acid residue 116 Y-->F ( TAC-->TTC) and a silent exchange at residue 121 K-->K (AAA-->AAG).

Real-time EEG-based detection of fatigue driving danger for accident prediction.

PubMed

Wang, Hong; Zhang, Chi; Shi, Tianwei; Wang, Fuwang; Ma, Shujun

2015-03-01

This paper proposes a real-time electroencephalogram (EEG)-based detection method of the potential danger during fatigue driving. To determine driver fatigue in real time, wavelet entropy with a sliding window and pulse coupled neural network (PCNN) were used to process the EEG signals in the visual area (the main information input route). To detect the fatigue danger, the neural mechanism of driver fatigue was analyzed. The functional brain networks were employed to track the fatigue impact on processing capacity of brain. The results show the overall functional connectivity of the subjects is weakened after long time driving tasks. The regularity is summarized as the fatigue convergence phenomenon. Based on the fatigue convergence phenomenon, we combined both the input and global synchronizations of brain together to calculate the residual amount of the information processing capacity of brain to obtain the dangerous points in real time. Finally, the danger detection system of the driver fatigue based on the neural mechanism was validated using accident EEG. The time distributions of the output danger points of the system have a good agreement with those of the real accident points.

Automated real-time needle-guide tracking for fast 3-T MR-guided transrectal prostate biopsy: a feasibility study.

PubMed

Zamecnik, Patrik; Schouten, Martijn G; Krafft, Axel J; Maier, Florian; Schlemmer, Heinz-Peter; Barentsz, Jelle O; Bock, Michael; Fütterer, Jurgen J

2014-12-01

To assess the feasibility of automatic needle-guide tracking by using a real-time phase-only cross correlation ( POCC phase-only cross correlation ) algorithm-based sequence for transrectal 3-T in-bore magnetic resonance (MR)-guided prostate biopsies. This study was approved by the ethics review board, and written informed consent was obtained from all patients. Eleven patients with a prostate-specific antigen level of at least 4 ng/mL (4 μg/L) and at least one transrectal ultrasonography-guided biopsy session with negative findings were enrolled. Regions suspicious for cancer were identified on 3-T multiparametric MR images. During a subsequent MR-guided biopsy, the regions suspicious for cancer were reidentified and targeted by using the POCC phase-only cross correlation -based tracking sequence. Besides testing a general technical feasibility of the biopsy procedure by using the POCC phase-only cross correlation -based tracking sequence, the procedure times were measured, and a pathologic analysis of the biopsy cores was performed. Thirty-eight core samples were obtained from 25 regions suspicious for cancer. It was technically feasible to perform the POCC phase-only cross correlation -based biopsies in all regions suspicious for cancer in each patient, with adequate biopsy samples obtained with each biopsy attempt. The median size of the region suspicious for cancer was 8 mm (range, 4-13 mm). In each region suspicious for cancer (median number per patient, two; range, 1-4), a median of one core sample per region was obtained (range, 1-3). The median time for guidance per target was 1.5 minutes (range, 0.7-5 minutes). Nineteen of 38 core biopsy samples contained cancer. This study shows that it is feasible to perform transrectal 3-T MR-guided biopsies by using a POCC phase-only cross correlation algorithm-based real-time tracking sequence. © RSNA, 2014.

A FRET-Based Real-Time PCR Assay to Identify the Main Causal Agents of New World Tegumentary Leishmaniasis

PubMed Central

De Los Santos, Maxy; Soberón, Valeria; Lucas, Carmen M.; Matlashewski, Greg; Llanos-Cuentas, Alejandro; Ore, Marianela; Baldeviano, G. Christian; Edgel, Kimberly A.; Lescano, Andres G.; Graf, Paul C. F.; Bacon, David J.

2013-01-01

In South America, various species of Leishmania are endemic and cause New World tegumentary leishmaniasis (NWTL). The correct identification of these species is critical for adequate clinical management and surveillance activities. We developed a real-time polymerase chain reaction (PCR) assay and evaluated its diagnostic performance using 64 archived parasite isolates and 192 prospectively identified samples collected from individuals with suspected leishmaniasis enrolled at two reference clinics in Lima, Peru. The real-time PCR assay was able to detect a single parasite and provided unambiguous melting peaks for five Leishmania species of the Viannia subgenus that are highly prevalent in South America: L. (V.) braziliensis, L. (V.) panamensis, L. (V.) guyanensis, L. (V.) peruviana and L. (V.) lainsoni. Using kinetoplastid DNA-based PCR as a gold standard, the real-time PCR had sensitivity and specificity values of 92% and 77%, respectively, which were significantly higher than those of conventional tests such as microscopy, culture and the leishmanin skin test (LST). In addition, the real-time PCR identified 147 different clinical samples at the species level, providing an overall agreement of 100% when compared to multilocus sequence typing (MLST) data performed on a subset of these samples. Furthermore, the real-time PCR was three times faster and five times less expensive when compared to PCR - MLST for species identification from clinical specimens. In summary, this new assay represents a cost-effective and reliable alternative for the identification of the main species causing NWTL in South America. PMID:23301111

Smartphone-Based Real-Time Indoor Location Tracking With 1-m Precision.

PubMed

Liang, Po-Chou; Krause, Paul

2016-05-01

Monitoring the activities of daily living of the elderly at home is widely recognized as useful for the detection of new or deteriorating health conditions. However, the accuracy of existing indoor location tracking systems remains unsatisfactory. The aim of this study was, therefore, to develop a localization system that can identify a patient's real-time location in a home environment with maximum estimation error of 2 m at a 95% confidence level. A proof-of-concept system based on a sensor fusion approach was built with considerations for lower cost, reduced intrusiveness, and higher mobility, deployability, and portability. This involved the development of both a step detector using the accelerometer and compass of an iPhone 5, and a radio-based localization subsystem using a Kalman filter and received signal strength indication to tackle issues that had been identified as limiting accuracy. The results of our experiments were promising with an average estimation error of 0.47 m. We are confident that with the proposed future work, our design can be adapted to a home-like environment with a more robust localization solution.

Application of real-time PCR and melting curve analysis in rapid Diego blood group genotyping.

PubMed

Novaretti, M C Z; Ruiz, A S; Dorlhiac-Llacer, P E; Chamone, D A F

2010-01-01

The paucity of appropriate reagents for serologic typing of the Diego blood group antigens has prompted the development of a real-time PCR and melting curve analysis for Diego blood group genotyping. In this study, we phenotyped 4326 donor blood samples for Di(a) using semiautomated equipment. All 157 Di(a+) samples were then genotyped by PCR using sequence-specific primers (PCR-SSP) for DI*02 because of anti-Di(b) scarcity. Of the 4326 samples, we simultaneously tested 160 samples for Di(a) and Di(b) serology, and DI*01 and DI*02 by PCR-SSP and by real-time PCR. We used the same primers for Diego genotyping by real-time PCR and PCR-SSP. Melting curve profiles obtained using the dissociation software of the real-time PCR apparatus enabled the discrimination of Diego alleles. Of the total samples tested, 4169 blood donors, 96.4 percent (95% confidence interval [CI], 95.8-96.9%), were homozygous for DI*02 and 157, 3.6 percent (95% CI, 3.1%-4.2%), were heterozygous DI*01/02. No blood donor was found to be homozygous for DI*01 in this study. The calculated DI*01 and DI*02 allele frequencies were 0.0181 (95% CI, 0.0173-0.0189) and 0.9819 (95% CI, 0.9791-0.9847), respectively, showing a good fit for the Hardy-Weinberg equilibrium. There was full concordance among Diego phenotype results by PCR-SSP and real-time PCR. DI*01 and DI*02 allele determination with SYBR Green I and thermal cycler technology are useful methods for Diego determination. The real-time PCR with SYBR Green I melting temperature protocol can be used as a rapid screening tool for DI*01 and DI*02 blood group genotyping.

Impact of Storage Time on Hepatitis B Virus DNA Stability in Clinical Specimens Determined by Quantitative Real-time PCR.

PubMed

Zhang, Xiaolian; Yang, Dongmei; Lu, Yu; Lao, Xianjun; Qin, Xue; Li, Shan

2016-01-01

Detecting blood levels of hepatitis B virus (HBV) DNA must be accurate and credible. Shipment and storage conditions of clinical samples affect the quality of nucleic acids and can interfere with HBV DNA analysis. The aim of our study was to compare HBV DNA stability in plasma specimens at 4 degrees C for different storage periods. Blood samples from 30 hepatitis B surface antigen (HBsAg) positive patients were collected in tubes containing EDTA-K2. Each sample was divided into eight aliquots, one of which was measured immediately for the initial viral load. The remaining aliquots were then stored at 4 degrees C and assessed after 1, 2, 3, 7, 14, 21, and 30 days of storage. Quantification of HBV DNA was performed by real-time polymerase chain reaction (RT-PCR), and the difference in HBV DNA concentrations between two different time points was analysed with a paired-samples t-test. HBV DNA was measured in a range of 2.00 - 8.00 IU/mL, with low within-run and between-run coefficients of variation (< 10%). Storing plasma for one month at 4 degrees C revealed no significant decrease in HBV DNA level (p = 0.231), and no trend was evident to indicate continued reduction over a 3-week storage period. Based on the results of this study, storing plasma for up to one month at 4 degrees C does not affect the stability of HBV DNA, regardless of the initial viral load.

Poliovirus replication proteins: RNA sequence encoding P3-1b and the sites of proteolytic processing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Semler, B.L.; Anderson, C.W.; Kitamura, N.

1981-06-01

A partial amino-terminal amino acid sequence of each of the major proteins encoded by the replicase region of the poliovirus genome has been determined. A comparison of this sequence information with the amino acid sequence predicted from the RNA sequence that has been determined for the 3' region of the poliovirus genome has allowed us to locate precisely the proteolytic cleavage sites at which the initial polyprotein is processed to create the poliovirus products P3-1b (NCVP1b), P3-2 (NCVP2), P3-4b (NCVP4b), and P3-7c (NCVP7c). For each of these products, as well as for the small genome-linked protein VPg, proteolytic cleavage occursmore » between a glutamine and a glycine residue to create the amino terminus of each protein. This result suggests that a single proteinase may be responsible for all of these cleavages. The sequence data also allow the precise positioning of the genome-linked protein VPg within the precursor P3-1b just proximal to the amino terminus of polypeptide P3-2.« less

A fully automated microfluidic-based electrochemical sensor for real-time bacteria detection.

PubMed

Altintas, Zeynep; Akgun, Mete; Kokturk, Guzin; Uludag, Yildiz

2018-02-15

A fully automated microfluidic-based electrochemical biosensor was designed and manufactured for pathogen detection. The quantification of Escherichia coli was investigated with standard and nanomaterial amplified immunoassays in the concentration ranges of 0.99 × 10 4 3.98 × 10 9 cfu mL -1 and 103.97 × 10 7 cfu mL -1 which resulted in detection limits of 1.99 × 10 4 cfu mL -1 and 50 cfu mL -1 , respectively. The developed methodology was then applied for E. coli quantification in water samples using nanomaterial modified assay. Same detection limit for E. coli was achieved for real sample analysis with a little decrease on the sensor signal. Cross-reactivity studies were conducted by testing Shigella, Salmonella spp., Salmonella typhimurium and Staphylococcus aureus on E. coli specific antibody surface that confirmed the high specificity of the developed immunoassays. The sensor surface could be regenerated multiple times which significantly reduces the cost of the system. Our custom-designed biosensor is capable of detecting bacteria with high sensitivity and specificity, and can serve as a promising tool for pathogen detection. Copyright © 2017 Elsevier B.V. All rights reserved.

Near real-time digital holographic microscope based on GPU parallel computing

NASA Astrophysics Data System (ADS)

Zhu, Gang; Zhao, Zhixiong; Wang, Huarui; Yang, Yan

2018-01-01

A transmission near real-time digital holographic microscope with in-line and off-axis light path is presented, in which the parallel computing technology based on compute unified device architecture (CUDA) and digital holographic microscopy are combined. Compared to other holographic microscopes, which have to implement reconstruction in multiple focal planes and are time-consuming the reconstruction speed of the near real-time digital holographic microscope can be greatly improved with the parallel computing technology based on CUDA, so it is especially suitable for measurements of particle field in micrometer and nanometer scale. Simulations and experiments show that the proposed transmission digital holographic microscope can accurately measure and display the velocity of particle field in micrometer scale, and the average velocity error is lower than 10%.With the graphic processing units(GPU), the computing time of the 100 reconstruction planes(512×512 grids) is lower than 120ms, while it is 4.9s using traditional reconstruction method by CPU. The reconstruction speed has been raised by 40 times. In other words, it can handle holograms at 8.3 frames per second and the near real-time measurement and display of particle velocity field are realized. The real-time three-dimensional reconstruction of particle velocity field is expected to achieve by further optimization of software and hardware. Keywords: digital holographic microscope,

Real-time FPGA-based radar imaging for smart mobility systems

NASA Astrophysics Data System (ADS)

Saponara, Sergio; Neri, Bruno

2016-04-01

The paper presents an X-band FMCW (Frequency Modulated Continuous Wave) Radar Imaging system, called X-FRI, for surveillance in smart mobility applications. X-FRI allows for detecting the presence of targets (e.g. obstacles in a railway crossing or urban road crossing, or ships in a small harbor), as well as their speed and their position. With respect to alternative solutions based on LIDAR or camera systems, X-FRI operates in real-time also in bad lighting and weather conditions, night and day. The radio-frequency transceiver is realized through COTS (Commercial Off The Shelf) components on a single-board. An FPGA-based baseband platform allows for real-time Radar image processing.

Coexistence of Epstein-Barr virus and Parvovirus B19 in tonsillar tissue samples: quantitative measurement by real-time PCR.

PubMed

Sahiner, Fatih; Gümral, Ramazan; Yildizoğlu, Üzeyir; Babayiğit, Mustafa Alparslan; Durmaz, Abdullah; Yiğit, Nuri; Saraçli, Mehmet Ali; Kubar, Ayhan

2014-08-01

In this study, we aimed to investigate the presence and copy number of six different viruses in tonsillar tissue samples removed surgically because of chronic recurrent tonsillitis or chronic obstructive tonsillar hypertrophy. In total, 56 tissue samples (tonsillar core) collected from 44 children and 12 adults were included in this study. The presence of viruses was investigated using a new TaqMan-based quantitative real-time PCR assay. Of the 56 tissue samples, 67.9% (38/56) were positive for at least one of the six viruses. Epstein-Barr virus was the most frequently detected virus, being found in 53.6% (30/56), followed by human Parvovirus B19 21.4% (12/56), human adenovirus 12.5% (7/56), human Cytomegalovirus 5.4% (3/56), BK polyomavirus 1.8% (1/56), and Herpes simplex virus 1.8% (1/56). Precancerous or cancerous changes were not detected in the tonsillar tissue samples by pathologic examination, whereas lymphoid hyperplasia was observed in 24 patients. In contrast to other viruses, B19 virus was present in high copy number in tonsillar tissues. The rates of EBV and B19 virus with high copy number (>500.000 copies/ml) were higher in children than in adults, and a positive relationship was also found between the presence of EBV and the presence of B19 virus with high copy number (P=0.037). It is previously reported that some viral agents are associated with different chronic tonsillar pathologies. In the present study, the presence of B19 virus in tonsillar core samples was investigated quantitatively for the first time, and our data suggests that EBV infections could be associated with B19 virus infections or could facilitate B19 virus replication. However, further detailed studies are needed to clarify this observation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Development of a SYBR Green I-based real-time PCR for detection of elephant endotheliotropic herpesvirus 1 infection in Asian elephants (Elephas maximus).

PubMed

Sariya, Ladawan; Chatsirivech, Jarin; Suksai, Parut; Wiriyarat, Witthawat; Songjaeng, Adisak; Tangsudjai, Siriporn; Kanthasaewee, Oraphan; Maikaew, Umaporn; Chaichoun, Kridsada

2012-10-01

Elephant endotheliotropic herpesvirus 1 (EEHV1) can cause fatal hemorrhagic disease in Asian elephants (Elephas maximus). Several studies have described this virus as a major threat to young Asian elephants. A SYBR Green I-based real-time polymerase chain reaction (PCR) was developed to identify EEHV1 on trunk swabs and necropsied tissues. Two of 29 (6.9%) trunk swab samples from healthy Asian elephants were positive for EEHV1. The viruses were analyzed and classified as EEHV1A based on 231 nucleotides of the terminase gene. Necropsied spleen and heart tissue showed the highest level and second highest levels of DNA virus copy accumulation, respectively. The detection limit of the test was 276 copies/μl of DNA. There was no cross-reaction with other mammalian herpesviruses, such as herpes simplex virus 1 and equine herpesvirus 2. Inter- and intra-assay showed low coefficients of variation values indicating the reproducibility of the test. The results indicated that the test can be practically used for epidemiological study, clinical diagnosis, and management and control of EEHV1. Copyright © 2012 Elsevier B.V. All rights reserved.

Repertoire of novel sequence signatures for the detection of Candidatus Liberibacter asiaticus by quantitative real-time PCR

PubMed Central

2014-01-01

Background Huanglongbing (HLB) or citrus greening is a devastating disease of citrus. The gram-negative bacterium Candidatus Liberibacter asiaticus (Las) belonging to the α-proteobacteria is responsible for HLB in North America as well as in Asia. Currently, there is no cure for this disease. Early detection and quarantine of Las-infected trees are important management strategies used to prevent HLB from invading HLB-free citrus producing regions. Quantitative real-time PCR (qRT-PCR) based molecular diagnostic assays have been routinely used in the detection and diagnosis of Las. The oligonucleotide primer pairs based on conserved genes or regions, which include 16S rDNA and the β-operon, have been widely employed in the detection of Las by qRT-PCR. The availability of whole genome sequence of Las now allows the design of primers beyond the conserved regions for the detection of Las explicitly. Results We took a complimentary approach by systematically screening the genes in a genome-wide fashion, to identify the unique signatures that are only present in Las by an exhaustive sequence based similarity search against the nucleotide sequence database. Our search resulted in 34 probable unique signatures. Furthermore, by designing the primer pair specific to the identified signatures, we showed that most of our primer sets are able to detect Las from the infected plant and psyllid materials collected from the USA and China by qRT-PCR. Overall, 18 primer pairs of the 34 are found to be highly specific to Las with no cross reactivity to the closely related species Ca. L. americanus (Lam) and Ca. L. africanus (Laf). Conclusions We have designed qRT-PCR primers based on Las specific genes. Among them, 18 are suitable for the detection of Las from Las-infected plant and psyllid samples. The repertoire of primers that we have developed and characterized in this study enhanced the qRT-PCR based molecular diagnosis of HLB. PMID:24533511

Real-time software-based end-to-end wireless visual communications simulation platform

NASA Astrophysics Data System (ADS)

Chen, Ting-Chung; Chang, Li-Fung; Wong, Andria H.; Sun, Ming-Ting; Hsing, T. Russell

1995-04-01

Wireless channel impairments pose many challenges to real-time visual communications. In this paper, we describe a real-time software based wireless visual communications simulation platform which can be used for performance evaluation in real-time. This simulation platform consists of two personal computers serving as hosts. Major components of each PC host include a real-time programmable video code, a wireless channel simulator, and a network interface for data transport between the two hosts. The three major components are interfaced in real-time to show the interaction of various wireless channels and video coding algorithms. The programmable features in the above components allow users to do performance evaluation of user-controlled wireless channel effects without physically carrying out these experiments which are limited in scope, time-consuming, and costly. Using this simulation platform as a testbed, we have experimented with several wireless channel effects including Rayleigh fading, antenna diversity, channel filtering, symbol timing, modulation, and packet loss.

Real-time generation of infrared ocean scene based on GPU

NASA Astrophysics Data System (ADS)

Jiang, Zhaoyi; Wang, Xun; Lin, Yun; Jin, Jianqiu

2007-12-01

Infrared (IR) image synthesis for ocean scene has become more and more important nowadays, especially for remote sensing and military application. Although a number of works present ready-to-use simulations, those techniques cover only a few possible ways of water interacting with the environment. And the detail calculation of ocean temperature is rarely considered by previous investigators. With the advance of programmable features of graphic card, many algorithms previously limited to offline processing have become feasible for real-time usage. In this paper, we propose an efficient algorithm for real-time rendering of infrared ocean scene using the newest features of programmable graphics processors (GPU). It differs from previous works in three aspects: adaptive GPU-based ocean surface tessellation, sophisticated balance equation of thermal balance for ocean surface, and GPU-based rendering for infrared ocean scene. Finally some results of infrared image are shown, which are in good accordance with real images.

Development of a highly sensitive one-tube nested real-time PCR for detecting Mycobacterium tuberculosis.

PubMed

Choi, Yeonim; Jeon, Bo-Young; Shim, Tae Sun; Jin, Hyunwoo; Cho, Sang-Nae; Lee, Hyeyoung

2014-12-01

Rapid, accurate detection of Mycobacterium tuberculosis is crucial in the diagnosis of tuberculosis (TB), but conventional diagnostic methods have limited sensitivity and specificity or are time consuming. A new highly sensitive nucleic acid amplification test, combined nested and real-time polymerase chain reaction (PCR) in a single tube (one-tube nested real-time PCR), was developed for detecting M. tuberculosis, which takes advantage of two PCR techniques, i.e., nested PCR and real-time PCR. One-tube nested real-time PCR was designed to have two sequential reactions with two sets of primers and dual probes for the insertion sequence (IS) 6110 sequence of M. tuberculosis in a single closed tube. The minimum limits of detection of IS6110 real-time PCR and IS6110 one-tube nested real-time PCR were 100 fg/μL and 1 fg/μL of M. tuberculosis DNA, respectively. AdvanSure TB/non-tuberculous mycobacteria (NTM) real-time PCR, IS6110 real-time PCR, and two-tube nested real-time PCR showed 100% sensitivity and 100% specificity for clinical M. tuberculosis isolates and NTM isolates. In comparison, the sensitivities of AdvanSure TB/NTM real-time PCR, single IS6110 real-time PCR, and one-tube nested real-time PCR were 91% (152/167), 94.6% (158/167), and 100% (167/167) for sputum specimens, respectively. In conclusion, IS6110 one-tube nested real-time PCR is useful for detecting M. tuberculosis due to its high sensitivity and simple manipulation. Copyright © 2014 Elsevier Inc. All rights reserved.

RAPHIDOPHYCEAE [CHADEFAUD EX SILVA] SYSTEMATICS AND RAPID IDENTIFICATION: SEQUENCE ANALYSES AND REAL-TIME PCR ASSAYS

PubMed Central

Bowers, Holly A.; Tomas, Carmelo; Tengs, Torstein; Kempton, Jason W.; Lewitus, Alan J.; Oldach, David W.

2010-01-01

Species within the class Raphidophyceae were associated with fish kill events in Japanese, European, Canadian, and U.S. coastal waters. Fish mortality was attributable to gill damage with exposure to reactive oxygen species (peroxide, superoxide, and hydroxide radicals), neurotoxins, physical clogging, and hemolytic substances. Morphological identification of these organisms in environmental water samples is difficult, particularly when fixatives are used. Because of this difficulty and the continued global emergence of these species in coastal estuarine waters, we initiated the development and validation of a suite of real-time polymerase chain reaction (PCR) assays. Sequencing was used to generate complete data sets for nuclear encoded small-subunit ribosomal RNA (SSU rRNA; 18S); internal transcribed spacers 1 and 2, 5.8S; and plastid encoded SSU rRNA (16S) for confirmed raphidophyte cultures from various geographic locations. Sequences for several Chattonella species (C. antiqua, C. marina, C. ovata, C. subsalsa, and C. verruculosa), Heterosigma akashiwo, and Fibrocapsa japonica were generated and used to design rapid and specific PCR assays for several species including C. verruculosa Hara et Chihara, C. subsalsa Biecheler, the complex comprised of C. marina Hara et Chihara, C. antiqua Ono and C. ovata, H. akashiwo Ono, and F. japonica Toriumi et Takano using appropriate loci. With this comprehensive data set, we were also able to perform phylogenetic analyses to determine the relationship between these species. PMID:20411032

Characterizing spatial heterogeneity based on the b-value and fractal analyses of the 2015 Nepal earthquake sequence

NASA Astrophysics Data System (ADS)

Nampally, Subhadra; Padhy, Simanchal; Dimri, Vijay P.

2018-01-01

The nature of spatial distribution of heterogeneities in the source area of the 2015 Nepal earthquake is characterized based on the seismic b-value and fractal analysis of its aftershocks. The earthquake size distribution of aftershocks gives a b-value of 1.11 ± 0.08, possibly representing the highly heterogeneous and low stress state of the region. The aftershocks exhibit a fractal structure characterized by a spectrum of generalized dimensions, Dq varying from D2 = 1.66 to D22 = 0.11. The existence of a fractal structure suggests that the spatial distribution of aftershocks is not a random phenomenon, but it self-organizes into a critical state, exhibiting a scale-independent structure governed by a power-law scaling, where a small perturbation in stress is sufficient enough to trigger aftershocks. In order to obtain the bias in fractal dimensions resulting from finite data size, we compared the multifractal spectrum for the real data and random simulations. On comparison, we found that the lower limit of bias in D2 is 0.44. The similarity in their multifractal spectra suggests the lack of long-range correlation in the data, with an only weakly multifractal or a monofractal with a single correlation dimension D2 characterizing the data. The minimum number of events required for a multifractal process with an acceptable error is discussed. We also tested for a possible correlation between changes in D2 and energy released during the earthquakes. The values of D2 rise during the two largest earthquakes (M > 7.0) in the sequence. The b- and D2 values are related by D2 = 1.45 b that corresponds to the intermediate to large earthquakes. Our results provide useful constraints on the spatial distribution of b- and D2-values, which are useful for seismic hazard assessment in the aftershock area of a large earthquake.

Real-time learning of predictive recognition categories that chunk sequences of items stored in working memory

PubMed Central

Kazerounian, Sohrob; Grossberg, Stephen

2014-01-01

How are sequences of events that are temporarily stored in a cognitive working memory unitized, or chunked, through learning? Such sequential learning is needed by the brain in order to enable language, spatial understanding, and motor skills to develop. In particular, how does the brain learn categories, or list chunks, that become selectively tuned to different temporal sequences of items in lists of variable length as they are stored in working memory, and how does this learning process occur in real time? The present article introduces a neural model that simulates learning of such list chunks. In this model, sequences of items are temporarily stored in an Item-and-Order, or competitive queuing, working memory before learning categorizes them using a categorization network, called a Masking Field, which is a self-similar, multiple-scale, recurrent on-center off-surround network that can weigh the evidence for variable-length sequences of items as they are stored in the working memory through time. A Masking Field hereby activates the learned list chunks that represent the most predictive item groupings at any time, while suppressing less predictive chunks. In a network with a given number of input items, all possible ordered sets of these item sequences, up to a fixed length, can be learned with unsupervised or supervised learning. The self-similar multiple-scale properties of Masking Fields interacting with an Item-and-Order working memory provide a natural explanation of George Miller's Magical Number Seven and Nelson Cowan's Magical Number Four. The article explains why linguistic, spatial, and action event sequences may all be stored by Item-and-Order working memories that obey similar design principles, and thus how the current results may apply across modalities. Item-and-Order properties may readily be extended to Item-Order-Rank working memories in which the same item can be stored in multiple list positions, or ranks, as in the list ABADBD. Comparisons

Single reaction, real time RT-PCR detection of all known avian and human metapneumoviruses.

PubMed

Lemaitre, E; Allée, C; Vabret, A; Eterradossi, N; Brown, P A

2018-01-01

Current molecular methods for the detection of avian and human metapneumovirus (AMPV, HMPV) are specifically targeted towards each virus species or individual subgroups of these. Here a broad range SYBR Green I real time RT-PCR was developed which amplified a highly conserved fragment of sequence in the N open reading frame. This method was sufficiently efficient and specific in detecting all MPVs. Its validation according to the NF U47-600 norm for the four AMPV subgroups estimated low limits of detection between 1000 and 10copies/μL, similar with detection levels described previously for real time RT-PCRs targeting specific subgroups. RNA viruses present a challenge for the design of durable molecular diagnostic test due to the rate of change in their genome sequences which can vary substantially in different areas and over time. The fact that the regions of sequence for primer hybridization in the described method have remained sufficiently conserved since the AMPV and HMPV diverged, should give the best chance of continued detection of current subgroups and of potential unknown or future emerging MPV strains. Copyright © 2017 Elsevier B.V. All rights reserved.

FPGA Based "Intelligent Tap" Device for Real-Time Ethernet Network Monitoring

NASA Astrophysics Data System (ADS)

Cupek, Rafał; Piękoś, Piotr; Poczobutt, Marcin; Ziębiński, Adam

This paper describes an "Intelligent Tap" - hardware device dedicated to support real-time Ethernet networks monitoring. Presented solution was created as a student project realized in Institute of Informatics, Silesian University of Technology with support from Softing A.G company. Authors provide description of realized FPGA based "Intelligent Tap" architecture dedicated for Real-Time Ethernet network monitoring systems. The practical device realization and feasibility study conclusions are presented also.

Quantitation of hepatitis B virus DNA in plasma using a sensitive cost-effective "in-house" real-time PCR assay.

PubMed

Daniel, Hubert Darius J; Fletcher, John G; Chandy, George M; Abraham, Priya

2009-01-01

Sensitive nucleic acid testing for the detection and accurate quantitation of hepatitis B virus (HBV) is necessary to reduce transmission through blood and blood products and for monitoring patients on antiviral therapy. The aim of this study is to standardize an "in-house" real-time HBV polymerase chain reaction (PCR) for accurate quantitation and screening of HBV. The "in-house" real-time assay was compared with a commercial assay using 30 chronically infected individuals and 70 blood donors who are negative for hepatitis B surface antigen, hepatitis C virus (HCV) antibody and human immunodeficiency virus (HIV) antibody. Further, 30 HBV-genotyped samples were tested to evaluate the "in-house" assay's capacity to detect genotypes prevalent among individuals attending this tertiary care hospital. The lower limit of detection of this "in-house" HBV real-time PCR was assessed against the WHO international standard and found to be 50 IU/mL. The interassay and intra-assay coefficient of variation (CV) of this "in-house" assay ranged from 1.4% to 9.4% and 0.0% to 2.3%, respectively. Virus loads as estimated with this "in-house" HBV real-time assay correlated well with the commercial artus HBV RG PCR assay ( r = 0.95, P < 0.0001). This assay can be used for the detection and accurate quantitation of HBV viral loads in plasma samples. This assay can be employed for the screening of blood donations and can potentially be adapted to a multiplex format for simultaneous detection of HBV, HIV and HCV to reduce the cost of testing in blood banks.

A video-based real-time adaptive vehicle-counting system for urban roads.

PubMed

Liu, Fei; Zeng, Zhiyuan; Jiang, Rong

2017-01-01

In developing nations, many expanding cities are facing challenges that result from the overwhelming numbers of people and vehicles. Collecting real-time, reliable and precise traffic flow information is crucial for urban traffic management. The main purpose of this paper is to develop an adaptive model that can assess the real-time vehicle counts on urban roads using computer vision technologies. This paper proposes an automatic real-time background update algorithm for vehicle detection and an adaptive pattern for vehicle counting based on the virtual loop and detection line methods. In addition, a new robust detection method is introduced to monitor the real-time traffic congestion state of road section. A prototype system has been developed and installed on an urban road for testing. The results show that the system is robust, with a real-time counting accuracy exceeding 99% in most field scenarios.

A video-based real-time adaptive vehicle-counting system for urban roads

PubMed Central

2017-01-01

In developing nations, many expanding cities are facing challenges that result from the overwhelming numbers of people and vehicles. Collecting real-time, reliable and precise traffic flow information is crucial for urban traffic management. The main purpose of this paper is to develop an adaptive model that can assess the real-time vehicle counts on urban roads using computer vision technologies. This paper proposes an automatic real-time background update algorithm for vehicle detection and an adaptive pattern for vehicle counting based on the virtual loop and detection line methods. In addition, a new robust detection method is introduced to monitor the real-time traffic congestion state of road section. A prototype system has been developed and installed on an urban road for testing. The results show that the system is robust, with a real-time counting accuracy exceeding 99% in most field scenarios. PMID:29135984

Assessment of cardiac time intervals using high temporal resolution real-time spiral phase contrast with UNFOLDed-SENSE.

PubMed

Kowalik, Grzegorz T; Knight, Daniel S; Steeden, Jennifer A; Tann, Oliver; Odille, Freddy; Atkinson, David; Taylor, Andrew; Muthurangu, Vivek

2015-02-01

To develop a real-time phase contrast MR sequence with high enough temporal resolution to assess cardiac time intervals. The sequence utilized spiral trajectories with an acquisition strategy that allowed a combination of temporal encoding (Unaliasing by fourier-encoding the overlaps using the temporal dimension; UNFOLD) and parallel imaging (Sensitivity encoding; SENSE) to be used (UNFOLDed-SENSE). An in silico experiment was performed to determine the optimum UNFOLD filter. In vitro experiments were carried out to validate the accuracy of time intervals calculation and peak mean velocity quantification. In addition, 15 healthy volunteers were imaged with the new sequence, and cardiac time intervals were compared to reference standard Doppler echocardiography measures. For comparison, in silico, in vitro, and in vivo experiments were also carried out using sliding window reconstructions. The in vitro experiments demonstrated good agreement between real-time spiral UNFOLDed-SENSE phase contrast MR and the reference standard measurements of velocity and time intervals. The protocol was successfully performed in all volunteers. Subsequent measurement of time intervals produced values in keeping with literature values and good agreement with the gold standard echocardiography. Importantly, the proposed UNFOLDed-SENSE sequence outperformed the sliding window reconstructions. Cardiac time intervals can be successfully assessed with UNFOLDed-SENSE real-time spiral phase contrast. Real-time MR assessment of cardiac time intervals may be beneficial in assessment of patients with cardiac conditions such as diastolic dysfunction. © 2014 Wiley Periodicals, Inc.

Real-time label-free quantitative fluorescence microscopy-based detection of ATP using a tunable fluorescent nano-aptasensor platform

NASA Astrophysics Data System (ADS)

Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung

2015-11-01

Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (r

Real-time distributed video coding for 1K-pixel visual sensor networks

NASA Astrophysics Data System (ADS)

Hanca, Jan; Deligiannis, Nikos; Munteanu, Adrian

2016-07-01

Many applications in visual sensor networks (VSNs) demand the low-cost wireless transmission of video data. In this context, distributed video coding (DVC) has proven its potential to achieve state-of-the-art compression performance while maintaining low computational complexity of the encoder. Despite their proven capabilities, current DVC solutions overlook hardware constraints, and this renders them unsuitable for practical implementations. This paper introduces a DVC architecture that offers highly efficient wireless communication in real-world VSNs. The design takes into account the severe computational and memory constraints imposed by practical implementations on low-resolution visual sensors. We study performance-complexity trade-offs for feedback-channel removal, propose learning-based techniques for rate allocation, and investigate various simplifications of side information generation yielding real-time decoding. The proposed system is evaluated against H.264/AVC intra, Motion-JPEG, and our previously designed DVC prototype for low-resolution visual sensors. Extensive experimental results on various data show significant improvements in multiple configurations. The proposed encoder achieves real-time performance on a 1k-pixel visual sensor mote. Real-time decoding is performed on a Raspberry Pi single-board computer or a low-end notebook PC. To the best of our knowledge, the proposed codec is the first practical DVC deployment on low-resolution VSNs.

Near real-time monitoring of UT1 with geodetic VLBI

NASA Astrophysics Data System (ADS)

Haas, R.; Hobiger, T.; Sekido, M.; Koyama, Y.; Kondo, T.; Takiguchi, H.; Kurihara, S.; Kokado, K.; Tanimoto, D.; Nozawa, K.; Wagner, J.; Ritakari, J.; Mujunen, A.; Uunila, M.

2011-07-01

Geodetic VLBI is unique among the geodetic space techniques since it provides a direct connection between the international terrestrial reference frame and the international celestial reference frame. The Earth rotation angle, usually expressed as UT1, can be determined directly from geodetic VLBI observations. Accurate information about the Earth rotation angle is necessary and important for navigation purposes, in particular for satellite missions and space navigation. A near real-time knowledge of UT1 with high accuracy is therefore highly desirable. During the last few years the advances in data transfer over high-speed optical fibre lines have made it possible to electronically send the observational data from a VLBI radio telescope on one side of the globe in real-time to a VLBI correlator on the other side of the globe. Thus, data of two telescopes on opposite sides of the Earth, forming a long east-west oriented baseline, can be correlated in near real-time. Furthermore, advances in automated processing of the correlation results have made it possible to derive the Earth rotation angle UT1 in near real-time. Since 2007, the VLBI research groups in Sweden, Finland and Japan collaborate to derive UT1 in near real-time. Several dedicated so-called ultra-rapid UT1-sessions with 1-2 hours duration were performed. It was shown that final UT1-results can be derived within a few minutes after the end of an observing session (Sekido et al., 2008; Matsuzaka et al., 2008). The quality of the UT1-results is on the same level as the so-called IERS rapid solutions, but with a much lower latency (Haas et al., 2010). Recently, the ultra-rapid approach has been applied to standard 24 hour long VLBI observing sessions that are organized by the International VLBI Service for Geodesy and Astrometry (IVS). The long east-west baseline between Onsala (Sweden) and Tsukuba (Japan) is used to derive UT1 with a sliding window approach already during the ongoing IVS-session. The data

Digital video timing analyzer for the evaluation of PC-based real-time simulation systems

NASA Astrophysics Data System (ADS)

Jones, Shawn R.; Crosby, Jay L.; Terry, John E., Jr.

2009-05-01

Due to the rapid acceleration in technology and the drop in costs, the use of commercial off-the-shelf (COTS) PC-based hardware and software components for digital and hardware-in-the-loop (HWIL) simulations has increased. However, the increase in PC-based components creates new challenges for HWIL test facilities such as cost-effective hardware and software selection, system configuration and integration, performance testing, and simulation verification/validation. This paper will discuss how the Digital Video Timing Analyzer (DiViTA) installed in the Aviation and Missile Research, Development and Engineering Center (AMRDEC) provides quantitative characterization data for PC-based real-time scene generation systems. An overview of the DiViTA is provided followed by details on measurement techniques, applications, and real-world examples of system benefits.

Timing, sequencing, and executive control in repetitive movement production.

PubMed

Krampe, Ralf Th; Mayr, Ulrich; Kliegl, Reinhold

2005-06-01

The authors demonstrate that the timing and sequencing of target durations require low-level timing and executive control. Sixteen young (M-sub(age) = 19 years) and 16 older (M-sub(age) = 70 years) adults participated in 2 experiments. In Experiment 1, individual mean-variance functions for low-level timing (isochronous tapping) and the sequencing of multiple targets (rhythm production) revealed (a) a dissociation of low-level timing and sequencing in both age groups, (b) negligible age differences for low-level timing, and (c) large age differences for sequencing. Experiment 2 supported the distinction between low-level timing and executive functions: Selection against a dominant rhythm and switching between rhythms impaired performances in both age groups and induced pronounced perseveration of the dominant pattern in older adults. ((c) 2005 APA, all rights reserved).

Diagnosing and Reconstructing Real-World Hydroclimatic Dynamics from Time Sequenced Data: The Case of Saltwater Intrusion into Coastal Wetlands in Everglades National Park

NASA Astrophysics Data System (ADS)

Huffaker, R.; Munoz-Carpena, R.

2016-12-01

There are increasing calls to audit decision-support models used for environmental policy to ensure that they correspond with the reality facing policy makers. Modelers can establish correspondence by providing empirical evidence of real-world dynamic behavior that their models skillfully simulate. We present a pre-modeling diagnostic framework—based on nonlinear dynamic analysis—for detecting and reconstructing real-world environmental dynamics from observed time-sequenced data. Phenomenological (data-driven) modeling—based on machine learning regression techniques—extracts a set of ordinary differential equations governing empirically-diagnosed system dynamics from a single time series, or from multiple time series on causally-interacting variables. We apply the framework to investigate saltwater intrusion into coastal wetlands in Everglades National Park, Florida, USA. We test the following hypotheses posed in the literature linking regional hydrologic variables with global climatic teleconnections: (1) Sea level in Florida Bay drives well level and well salinity in the coastal Everglades; (2) Atlantic Multidecadal Oscillation (AMO) drives sea level, well level and well salinity; and (3) AMO and (El Niño Southern Oscillation) ENSO bi-causally interact. The thinking is that salt water intrusion links ocean-surface salinity with salinity of inland water sources, and sea level with inland water; that AMO and ENSO share a teleconnective relationship (perhaps through the atmosphere); and that AMO and ENSO both influence inland precipitation and thus well levels. Our results support these hypotheses, and we successfully construct a parsimonious phenomenological model that reproduces diagnosed nonlinear dynamics and system interactions. We propose that reconstructed data dynamics be used, along with other expert information, as a rigorous benchmark to guide specification and testing of hydrologic decision support models corresponding with real-world behavior.

Real-time implementation of biofidelic SA1 model for tactile feedback.

PubMed

Russell, A F; Armiger, R S; Vogelstein, R J; Bensmaia, S J; Etienne-Cummings, R

2009-01-01

In order for the functionality of an upper-limb prosthesis to approach that of a real limb it must be able to, accurately and intuitively, convey sensory feedback to the limb user. This paper presents results of the real-time implementation of a 'biofidelic' model that describes mechanotransduction in Slowly Adapting Type 1 (SA1) afferent fibers. The model accurately predicts the timing of action potentials for arbitrary force or displacement stimuli and its output can be used as stimulation times for peripheral nerve stimulation by a neuroprosthetic device. The model performance was verified by comparing the predicted action potential (or spike) outputs against measured spike outputs for different vibratory stimuli. Furthermore experiments were conducted to show that, like real SA1 fibers, the model's spike rate varies according to input pressure and that a periodic 'tapping' stimulus evokes periodic spike outputs.

Real-Time Reliability Verification for UAV Flight Control System Supporting Airworthiness Certification.

PubMed

Xu, Haiyang; Wang, Ping

2016-01-01

In order to verify the real-time reliability of unmanned aerial vehicle (UAV) flight control system and comply with the airworthiness certification standard, we proposed a model-based integration framework for modeling and verification of time property. Combining with the advantages of MARTE, this framework uses class diagram to create the static model of software system, and utilizes state chart to create the dynamic model. In term of the defined transformation rules, the MARTE model could be transformed to formal integrated model, and the different part of the model could also be verified by using existing formal tools. For the real-time specifications of software system, we also proposed a generating algorithm for temporal logic formula, which could automatically extract real-time property from time-sensitive live sequence chart (TLSC). Finally, we modeled the simplified flight control system of UAV to check its real-time property. The results showed that the framework could be used to create the system model, as well as precisely analyze and verify the real-time reliability of UAV flight control system.

Real-Time Reliability Verification for UAV Flight Control System Supporting Airworthiness Certification

PubMed Central

Xu, Haiyang; Wang, Ping

2016-01-01

In order to verify the real-time reliability of unmanned aerial vehicle (UAV) flight control system and comply with the airworthiness certification standard, we proposed a model-based integration framework for modeling and verification of time property. Combining with the advantages of MARTE, this framework uses class diagram to create the static model of software system, and utilizes state chart to create the dynamic model. In term of the defined transformation rules, the MARTE model could be transformed to formal integrated model, and the different part of the model could also be verified by using existing formal tools. For the real-time specifications of software system, we also proposed a generating algorithm for temporal logic formula, which could automatically extract real-time property from time-sensitive live sequence chart (TLSC). Finally, we modeled the simplified flight control system of UAV to check its real-time property. The results showed that the framework could be used to create the system model, as well as precisely analyze and verify the real-time reliability of UAV flight control system. PMID:27918594

DNA microsatellite region for a reliable quantification of soft wheat adulteration in durum wheat-based foodstuffs by real-time PCR.

PubMed

Sonnante, Gabriella; Montemurro, Cinzia; Morgese, Anita; Sabetta, Wilma; Blanco, Antonio; Pasqualone, Antonella

2009-11-11

Italian industrial pasta and durum wheat typical breads must be prepared using exclusively durum wheat semolina. Previously, a microsatellite sequence specific of the wheat D-genome had been chosen for traceability of soft wheat in semolina and bread samples, using qualitative and quantitative Sybr green-based real-time experiments. In this work, we describe an improved method based on the same soft wheat genomic region by means of a quantitative real-time PCR using a dual-labeled probe. Standard curves based on dilutions of 100% soft wheat flour, pasta, or bread were constructed. Durum wheat semolina, pasta, and bread samples were prepared with increasing amounts of soft wheat to verify the accuracy of the method. Results show that reliable quantifications were obtained especially for the samples containing a lower amount of soft wheat DNA, fulfilling the need to verify labeling of pasta and typical durum wheat breads.

A first near real-time seismology-based landquake monitoring system.

PubMed

Chao, Wei-An; Wu, Yih-Min; Zhao, Li; Chen, Hongey; Chen, Yue-Gau; Chang, Jui-Ming; Lin, Che-Min

2017-03-02

Hazards from gravity-driven instabilities on hillslope (termed 'landquake' in this study) are an important problem facing us today. Rapid detection of landquake events is crucial for hazard mitigation and emergency response. Based on the real-time broadband data in Taiwan, we have developed a near real-time landquake monitoring system, which is a fully automatic process based on waveform inversion that yields source information (e.g., location and mechanism) and identifies the landquake source by examining waveform fitness for different types of source mechanisms. This system has been successfully tested offline using seismic records during the passage of the 2009 Typhoon Morakot in Taiwan and has been in online operation during the typhoon season in 2015. In practice, certain levels of station coverage (station gap < 180°), signal-to-noise ratio (SNR ≥ 5.0), and a threshold of event size (volume >10 6  m 3 and area > 0.20 km 2 ) are required to ensure good performance (fitness > 0.6 for successful source identification) of the system, which can be readily implemented in other places in the world with real-time seismic networks and high landquake activities.

A first near real-time seismology-based landquake monitoring system

PubMed Central

Chao, Wei-An; Wu, Yih-Min; Zhao, Li; Chen, Hongey; Chen, Yue-Gau; Chang, Jui-Ming; Lin, Che-Min

2017-01-01

Hazards from gravity-driven instabilities on hillslope (termed ‘landquake’ in this study) are an important problem facing us today. Rapid detection of landquake events is crucial for hazard mitigation and emergency response. Based on the real-time broadband data in Taiwan, we have developed a near real-time landquake monitoring system, which is a fully automatic process based on waveform inversion that yields source information (e.g., location and mechanism) and identifies the landquake source by examining waveform fitness for different types of source mechanisms. This system has been successfully tested offline using seismic records during the passage of the 2009 Typhoon Morakot in Taiwan and has been in online operation during the typhoon season in 2015. In practice, certain levels of station coverage (station gap < 180°), signal-to-noise ratio (SNR ≥ 5.0), and a threshold of event size (volume >106 m3 and area > 0.20 km2) are required to ensure good performance (fitness > 0.6 for successful source identification) of the system, which can be readily implemented in other places in the world with real-time seismic networks and high landquake activities. PMID:28252039

Real-time stylistic prediction for whole-body human motions.

PubMed

Matsubara, Takamitsu; Hyon, Sang-Ho; Morimoto, Jun

2012-01-01

The ability to predict human motion is crucial in several contexts such as human tracking by computer vision and the synthesis of human-like computer graphics. Previous work has focused on off-line processes with well-segmented data; however, many applications such as robotics require real-time control with efficient computation. In this paper, we propose a novel approach called real-time stylistic prediction for whole-body human motions to satisfy these requirements. This approach uses a novel generative model to represent a whole-body human motion including rhythmic motion (e.g., walking) and discrete motion (e.g., jumping). The generative model is composed of a low-dimensional state (phase) dynamics and a two-factor observation model, allowing it to capture the diversity of motion styles in humans. A real-time adaptation algorithm was derived to estimate both state variables and style parameter of the model from non-stationary unlabeled sequential observations. Moreover, with a simple modification, the algorithm allows real-time adaptation even from incomplete (partial) observations. Based on the estimated state and style, a future motion sequence can be accurately predicted. In our implementation, it takes less than 15 ms for both adaptation and prediction at each observation. Our real-time stylistic prediction was evaluated for human walking, running, and jumping behaviors. Copyright © 2011 Elsevier Ltd. All rights reserved.

Event-specific real-time detection and quantification of genetically modified Roundup Ready soybean.

PubMed

Huang, Chia-Chia; Pan, Tzu-Ming

2005-05-18

The event-specific real-time detection and quantification of Roundup Ready soybean (RRS) using an ABI PRISM 7700 sequence detection system with light upon extension (LUX) primer was developed in this study. The event-specific primers were designed, targeting the junction of the RRS 5' integration site and the endogenous gene lectin1. Then, a standard reference plasmid was constructed that carried both of the targeted sequences for quantitative analysis. The detection limit of the LUX real-time PCR system was 0.05 ng of 100% RRS genomic DNA, which was equal to 20.5 copies. The range of quantification was from 0.1 to 100%. The sensitivity and range of quantification successfully met the requirement of the labeling rules in the European Union and Taiwan.

Development of SYBR Green I Based Real-Time RT-PCR Assay for Specific Detection of Watermelon silver mottle Virus.

PubMed

Rao, Xueqin; Sun, Jie

2015-09-01

Watermelon silver mottle virus (WSMoV), which belongs to the genus Tospovirus , causes significant loss in Cucurbitaceae plants. Development of a highly sensitive and reliable detection method for WSMoV. Recombinant plasmids for targeting the sequence of nucleocapsid protein gene of WSMoV were constructed. SYBR Green I real-time PCR was established and evaluated with standard recombinant plasmids and 27 watermelon samples showing WSMoV infection symptoms. The recombinant plasmid was used as template for SYBR Green I real-time PCR to generate standard and melting curves. Melting curve analysis indicated no primer-dimers and non-specific products in the assay. No cross-reaction was observed with Capsicum chlorosis virus (genus Tospovirus ) and Cucumber mosaic virus (genus Cucumovirus). Repeatability tests indicated that inter-assay variability of the Ct values was 1.6%. A highly sensitive, reliable and rapid detection method of SYBR Green I real-time PCR for timely detection of WSMoV plants and vector thrips was established, which will facilitate disease forecast and control.

[Identifying and sequence analysis of HLA-B*2736].

PubMed

Li, Zhen; Zou, Hong-Yan; Shao, Chao-Peng; Tang, Si; Wang, Da-Ming; Cheng, Liang-Hong

2007-11-01

An unknown HLA-B allele which was similar to HLA-B*270401 was detected by FLOW-SSOPCR-SSP and heterozygous sequence-based typing (SBT) in Chinese Han individual. Its anomalous patterns suggested the possible presence of new allele. Amplifying exon 2-5(include intron 2-4) of the HLA-B*27 allele separately by using allele-specific primers and sequencing in both directions. Identifying the difference between the novel B*27 allele and B*270401. The sequence of novel B*27 from exon 2 to partial exon 5 is 1 815 bp. There are 10 nt changes from B*270401 in exon 3-4, at nt634where A-->C(codon130 AGC-->CGC, 130 S-->R); nt670 where A-->T (codon142 ACC-->TCC, 142 T-->S); nt683 where G-->T (codon146 TGG-->TTG, 146 W-->L); nt698 where A-->T (codon151 GAG-->GTG, 151 E-->V); nt774 where G-->C (codon176 GAG-->GAC, 176 E-->D); nt776 where C-->A (codon177 ACG-->AAG, 177 T-->K); nt781 where C-->G (codon179 CAG-->GAG, 179Q-->E); nt789 where G-->T (codon181 GCG-->GCT) resulting no coding change; nt1438 where C-->T (codon206 GGC-->GGT) resulting no coding change; nt1449 where G-->C (codon210 GGG-->GCG, 210G-->A). In IMGT/HLA database, only three alleles (B*270502/2706/2732) have sequences of introns. The same sequence in intron 2 showed homology between the novel HLA-B*27 allele and B*2706, but their homology could not be supported in intron 3-4. Comparing the sequence of the novel B*27 allele in intron 3 and 4 with B*27 group, it showed there are three mutations at nt106 C-->G, nt179 G-->A, nt536 G-->A and one deletion at nt168 in intron 3 and one mutations at nt82 T-->C in intron 4, but the sequence of the novel B*27 allele in intron 3 and 4 was all the same to B*070201. The sequence was submitted to Gen-Bank and the accession number was DQ915176. The allele has been confirmed as an extension of B*2736 by the WHO Nomenclature committee in November 2006.

Real-time visual simulation of APT system based on RTW and Vega

NASA Astrophysics Data System (ADS)

Xiong, Shuai; Fu, Chengyu; Tang, Tao

2012-10-01

The Matlab/Simulink simulation model of APT (acquisition, pointing and tracking) system is analyzed and established. Then the model's C code which can be used for real-time simulation is generated by RTW (Real-Time Workshop). Practical experiments show, the simulation result of running the C code is the same as running the Simulink model directly in the Matlab environment. MultiGen-Vega is a real-time 3D scene simulation software system. With it and OpenGL, the APT scene simulation platform is developed and used to render and display the virtual scenes of the APT system. To add some necessary graphics effects to the virtual scenes real-time, GLSL (OpenGL Shading Language) shaders are used based on programmable GPU. By calling the C code, the scene simulation platform can adjust the system parameters on-line and get APT system's real-time simulation data to drive the scenes. Practical application shows that this visual simulation platform has high efficiency, low charge and good simulation effect.

Real-time two-dimensional temperature imaging using ultrasound.

PubMed

Liu, Dalong; Ebbini, Emad S

2009-01-01

We present a system for real-time 2D imaging of temperature change in tissue media using pulse-echo ultrasound. The frontend of the system is a SonixRP ultrasound scanner with a research interface giving us the capability of controlling the beam sequence and accessing radio frequency (RF) data in real-time. The beamformed RF data is streamlined to the backend of the system, where the data is processed using a two-dimensional temperature estimation algorithm running in the graphics processing unit (GPU). The estimated temperature is displayed in real-time providing feedback that can be used for real-time control of the heating source. Currently we have verified our system with elastography tissue mimicking phantom and in vitro porcine heart tissue, excellent repeatability and sensitivity were demonstrated.

Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli.

PubMed

Hasanpour, Mojtaba; Najafi, Akram

2017-06-01

Uropathogenic Escherichia coli (UPEC) is among major pathogens causing 80-90% of all episodes of urinary tract infections (UTIs). Recently, E. coli strains are divided into eight main phylogenetic groups including A, B1, B2, C, D, E, F, and clade I. This study was aimed to develop a rapid, sensitive, and specific multiplex real time PCR method capable of detecting phylogenetic groups of E. coli strains. This study was carried out on E. coli strains (isolated from the patient with UTI) in which the presence of all seven target genes had been confirmed in our previous phylogenetic study. An EvaGreen-based singleplex and multiplex real-time PCR with melting curve analysis was designed for simultaneous detection and differentiation of these genes. The primers were selected mainly based on the production of amplicons with melting temperatures (T m ) ranging from 82°C to 93°C and temperature difference of more than 1.5°C between each peak.The multiplex real-time PCR assays that have been developed in the present study were successful in detecting the eight main phylogenetic groups. Seven distinct melting peaks were discriminated, with Tm value of 93±0.8 for arpA, 89.2±0.1for chuA, 86.5±0.1 for yjaA, 82.3±0.2 for TspE4C2, 87.8±0.1for trpAgpC, 85.4±0.6 for arpAgpE genes, and 91±0.5 for the internal control. To our knowledge, this study is the first melting curve-based real-time PCR assay developed for simultaneous and discrete detection of these seven target genes. Our findings showed that this assay has the potential to be a rapid, reliable and cost-effective alternative for routine phylotyping of E. coli strains. Copyright © 2017 Elsevier B.V. All rights reserved.

Using real-time PCR to specifically detect Burkholderia mallei.

PubMed

Ulrich, Melanie P; Norwood, David A; Christensen, Deanna R; Ulrich, Ricky L

2006-05-01

Burkholderia mallei is the causative agent of human and animal glanders and is a category B biothreat agent. Rapid diagnosis of B. mallei and immediate prophylactic treatment are essential for patient survival. The majority of current bacteriological and immunological techniques for identifying B. mallei from clinical samples are time-consuming, and cross-reactivity with closely related organisms (i.e. Burkholderia pseudomallei) is a problem. In this investigation, two B. mallei-specific real-time PCR assays targeting the B. mallei bimA(ma) gene (Burkholderia intracellular motility A; BMAA0749), which encodes a protein involved in actin polymerization, were developed. The PCR primer and probe sets were tested for specificity against a collection of B. mallei and B. pseudomallei isolates obtained from numerous clinical and environmental (B. pseudomallei only) sources. The assays were also tested for cross-reactivity using template DNA from 14 closely related Burkholderia species. The relative limit of detection for the assays was found to be 1 pg or 424 genome equivalents. The authors also analysed the applicability of assays to detect B. mallei within infected BALB/c mouse tissues. Beginning 1 h post aerosol exposure, B. mallei was successfully identified within the lungs, and starting at 24 h post exposure, in the spleen and liver. Surprisingly, B. mallei was not detected in the blood of acutely infected animals. This investigation provides two real-time PCR assays for the rapid and specific identification of B. mallei.

CortiQ-based Real-Time Functional Mapping for Epilepsy Surgery.

PubMed

Kapeller, Christoph; Korostenskaja, Milena; Prueckl, Robert; Chen, Po-Ching; Lee, Ki Heyeong; Westerveld, Michael; Salinas, Christine M; Cook, Jane C; Baumgartner, James E; Guger, Christoph

2015-06-01

To evaluate the use of the cortiQ-based mapping system (g.tec medication engineering GmbH, Austria) for real-time functional mapping (RTFM) and to compare it to results from electrical cortical stimulation mapping (ESM) and functional magnetic resonance imaging (fMRI). Electrocorticographic activity was recorded in 3 male patients with intractable epilepsy by using cortiQ mapping system and analyzed in real time. Activation related to motor, sensory, and receptive language tasks was determined by evaluating the power of the high gamma frequency band (60-170 Hz). The sensitivity and specificity of RTFM were tested against ESM and fMRI results. "Next-neighbor" approach demonstrated [sensitivity/specificity %] (1) RTFM against ESM: 100.00/79.70 for hand motor; 100.00/73.87 for hand sensory; -/87 for language (it was not identified by the ESM); (2) RTFM against fMRI: 100.00/84.4 for hand motor; 66.70/85.35 for hand sensory; and 87.85/77.70 for language. The results of the quantitative "next-neighbor" RTFM evaluation were concordant to those from ESM and fMRI. The RTFM correlates well with localization of hand motor function provided by ESM and fMRI, which may offer added localization in the operating room and guidance for extraoperative ESM mapping. Real-time functional mapping correlates with fMRI language activation when ESM findings are negative. It has fewer limitations than ESM and greater flexibility in activation paradigms and measuring responses.

Kinect based real-time position calibration for nasal endoscopic surgical navigation system

NASA Astrophysics Data System (ADS)

Fan, Jingfan; Yang, Jian; Chu, Yakui; Ma, Shaodong; Wang, Yongtian

2016-03-01

Unanticipated, reactive motion of the patient during skull based tumor resective surgery is the source of the consequence that the nasal endoscopic tracking system is compelled to be recalibrated. To accommodate the calibration process with patient's movement, this paper developed a Kinect based Real-time positional calibration method for nasal endoscopic surgical navigation system. In this method, a Kinect scanner was employed as the acquisition part of the point cloud volumetric reconstruction of the patient's head during surgery. Then, a convex hull based registration algorithm aligned the real-time image of the patient head with a model built upon the CT scans performed in the preoperative preparation to dynamically calibrate the tracking system if a movement was detected. Experimental results confirmed the robustness of the proposed method, presenting a total tracking error within 1 mm under the circumstance of relatively violent motions. These results point out the tracking accuracy can be retained stably and the potential to expedite the calibration of the tracking system against strong interfering conditions, demonstrating high suitability for a wide range of surgical applications.

Real-time numerical forecast of global epidemic spreading: case study of 2009 A/H1N1pdm.

PubMed

Tizzoni, Michele; Bajardi, Paolo; Poletto, Chiara; Ramasco, José J; Balcan, Duygu; Gonçalves, Bruno; Perra, Nicola; Colizza, Vittoria; Vespignani, Alessandro

2012-12-13

Mathematical and computational models for infectious diseases are increasingly used to support public-health decisions; however, their reliability is currently under debate. Real-time forecasts of epidemic spread using data-driven models have been hindered by the technical challenges posed by parameter estimation and validation. Data gathered for the 2009 H1N1 influenza crisis represent an unprecedented opportunity to validate real-time model predictions and define the main success criteria for different approaches. We used the Global Epidemic and Mobility Model to generate stochastic simulations of epidemic spread worldwide, yielding (among other measures) the incidence and seeding events at a daily resolution for 3,362 subpopulations in 220 countries. Using a Monte Carlo Maximum Likelihood analysis, the model provided an estimate of the seasonal transmission potential during the early phase of the H1N1 pandemic and generated ensemble forecasts for the activity peaks in the northern hemisphere in the fall/winter wave. These results were validated against the real-life surveillance data collected in 48 countries, and their robustness assessed by focusing on 1) the peak timing of the pandemic; 2) the level of spatial resolution allowed by the model; and 3) the clinical attack rate and the effectiveness of the vaccine. In addition, we studied the effect of data incompleteness on the prediction reliability. Real-time predictions of the peak timing are found to be in good agreement with the empirical data, showing strong robustness to data that may not be accessible in real time (such as pre-exposure immunity and adherence to vaccination campaigns), but that affect the predictions for the attack rates. The timing and spatial unfolding of the pandemic are critically sensitive to the level of mobility data integrated into the model. Our results show that large-scale models can be used to provide valuable real-time forecasts of influenza spreading, but they require high

A Programmable Microkernel for Real-Time Systems

DTIC Science & Technology

2003-06-01

A Programmable Microkernel for Real - Time Systems Christoph M. Kirsch Thomas A. Henzinger Marco A.A. Sanvido Report No. UCB/CSD-3-1250 June 2003...TITLE AND SUBTITLE A Programmable Microkernel for Real - Time Systems 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 A Programmable Microkernel for Real - Time Systems ∗ Christoph M

Demonstrating the Value of Near Real-time Satellite-based Earth Observations in a Research and Education Framework

NASA Astrophysics Data System (ADS)

Chiu, L.; Hao, X.; Kinter, J. L.; Stearn, G.; Aliani, M.

2017-12-01

The launch of GOES-16 series provides an opportunity to advance near real-time applications in natural hazard detection, monitoring and warning. This study demonstrates the capability and values of receiving real-time satellite-based Earth observations over a fast terrestrial networks and processing high-resolution remote sensing data in a university environment. The demonstration system includes 4 components: 1) Near real-time data receiving and processing; 2) data analysis and visualization; 3) event detection and monitoring; and 4) information dissemination. Various tools are developed and integrated to receive and process GRB data in near real-time, produce images and value-added data products, and detect and monitor extreme weather events such as hurricane, fire, flooding, fog, lightning, etc. A web-based application system is developed to disseminate near-real satellite images and data products. The images are generated with GIS-compatible format (GeoTIFF) to enable convenient use and integration in various GIS platforms. This study enhances the capacities for undergraduate and graduate education in Earth system and climate sciences, and related applications to understand the basic principles and technology in real-time applications with remote sensing measurements. It also provides an integrated platform for near real-time monitoring of extreme weather events, which are helpful for various user communities.

Connectivity-based neurofeedback: Dynamic causal modeling for real-time fMRI☆

PubMed Central

Koush, Yury; Rosa, Maria Joao; Robineau, Fabien; Heinen, Klaartje; W. Rieger, Sebastian; Weiskopf, Nikolaus; Vuilleumier, Patrik; Van De Ville, Dimitri; Scharnowski, Frank

2013-01-01

Neurofeedback based on real-time fMRI is an emerging technique that can be used to train voluntary control of brain activity. Such brain training has been shown to lead to behavioral effects that are specific to the functional role of the targeted brain area. However, real-time fMRI-based neurofeedback so far was limited to mainly training localized brain activity within a region of interest. Here, we overcome this limitation by presenting near real-time dynamic causal modeling in order to provide feedback information based on connectivity between brain areas rather than activity within a single brain area. Using a visual–spatial attention paradigm, we show that participants can voluntarily control a feedback signal that is based on the Bayesian model comparison between two predefined model alternatives, i.e. the connectivity between left visual cortex and left parietal cortex vs. the connectivity between right visual cortex and right parietal cortex. Our new approach thus allows for training voluntary control over specific functional brain networks. Because most mental functions and most neurological disorders are associated with network activity rather than with activity in a single brain region, this novel approach is an important methodological innovation in order to more directly target functionally relevant brain networks. PMID:23668967

Conjugated polyelectrolyte based real-time fluorescence assay for phospholipase C.

PubMed

Liu, Yan; Ogawa, Katsu; Schanze, Kirk S

2008-01-01

A fluorescence turnoff assay for phospholipase C (PLC) from Clostridium perfringens is developed based on the reversible interaction between the natural substrate, phosphatidylcholine, and a fluorescent, water-soluble conjugated polyelectrolyte (CPE). The fluorescence intensity of the CPE in water is increased substantially by the addition of the phospholipid due to the formation of a CPE-lipid complex. Incubation of the CPE-lipid complex with the enzyme PLC causes the fluorescence intensity to decrease (turnoff sensor); the response arises due to PLC-catalyzed hydrolysis of the phosphatidylcholine, which effectively disrupts the CPE-lipid complex. The PLC assay operates with phospholipid substrate concentrations in the micromolar range, and the analytical detection limit for PLC is <1 nM. The optimized assay provides a convenient, rapid, and real-time sensor for PLC activity. The real-time fluorescence intensity from the CPE can be converted to substrate concentration by using an ex situ calibration curve, allowing PLC-catalyzed reaction rates and kinetic parameters to be determined. PLC activation by Ca2+ and inhibition by EDTA and fluoride ion are demonstrated using the optimized sensor.

Real-time film recording from stroke-written CRT's

NASA Technical Reports Server (NTRS)

Hunt, R.; Grunwald, A. J.

1980-01-01

Real-time simulation studies often require motion-picture recording of events directly from stroke written cathode-ray tubes (CRT's). Difficulty presented is prevention of "flicker," which results from lack of synchronization between display sequence on CRT and shutter motion of camera. Programmable method has been devised for phasing display sequence to shutter motion, ensuring flicker-free recordings.

Sensitive quantification of aflatoxin B1 in animal feeds, corn feed grain, and yellow corn meal using immunomagnetic bead-based recovery and real-time immunoquantitative-PCR.

PubMed

Babu, Dinesh; Muriana, Peter M

2014-12-02

Aflatoxins are considered unavoidable natural mycotoxins encountered in foods, animal feeds, and feed grains. In this study, we demonstrate the application of our recently developed real-time immunoquantitative PCR (RT iq-PCR) assay for sensitive detection and quantification of aflatoxins in poultry feed, two types of dairy feed (1 and 2), horse feed, whole kernel corn feed grains, and retail yellow ground corn meal. Upon testing methanol/water (60:40) extractions of the above samples using competitive direct enzyme linked immunosorbent assay, the aflatoxin content was found to be <20 μg/kg. The RT iq-PCR assay exhibited high antigen hook effect in samples containing aflatoxin levels higher than the quantification limits (0.1-10 μg/kg), addressed by comparing the quantification results of undiluted and diluted extracts. In testing the reliability of the immuno-PCR assay, samples were spiked with 200 μg/kg of aflatoxin B1, but the recovery of spiked aflatoxin was found to be poor. Considering the significance of determining trace levels of aflatoxins and their serious implications for animal and human health, the RT iq-PCR method described in this study can be useful for quantifying low natural aflatoxin levels in complex matrices of food or animal feed samples without the requirement of extra sample cleanup.

Molecular beacon probes-base multiplex NASBA Real-time for detection of HIV-1 and HCV.

PubMed

Mohammadi-Yeganeh, S; Paryan, M; Mirab Samiee, S; Kia, V; Rezvan, H

2012-06-01

Developed in 1991, nucleic acid sequence-based amplification (NASBA) has been introduced as a rapid molecular diagnostic technique, where it has been shown to give quicker results than PCR, and it can also be more sensitive. This paper describes the development of a molecular beacon-based multiplex NASBA assay for simultaneous detection of HIV-1 and HCV in plasma samples. A well-conserved region in the HIV-1 pol gene and 5'-NCR of HCV genome were used for primers and molecular beacon design. The performance features of HCV/HIV-1 multiplex NASBA assay including analytical sensitivity and specificity, clinical sensitivity and clinical specificity were evaluated. The analysis of scalar concentrations of the samples indicated that the limit of quantification of the assay was <1000 copies/ml for HIV-1 and <500 copies/ml for HCV with 95% confidence interval. Multiplex NASBA assay showed a 98% sensitivity and 100% specificity. The analytical specificity study with BLAST software demonstrated that the primers do not attach to any other sequences except for that of HIV-1 or HCV. The primers and molecular beacon probes detected all HCV genotypes and all major variants of HIV-1. This method may represent a relatively inexpensive isothermal method for detection of HIV-1/HCV co-infection in monitoring of patients.

A framework for intelligent data acquisition and real-time database searching for shotgun proteomics.

PubMed

Graumann, Johannes; Scheltema, Richard A; Zhang, Yong; Cox, Jürgen; Mann, Matthias

2012-03-01

In the analysis of complex peptide mixtures by MS-based proteomics, many more peptides elute at any given time than can be identified and quantified by the mass spectrometer. This makes it desirable to optimally allocate peptide sequencing and narrow mass range quantification events. In computer science, intelligent agents are frequently used to make autonomous decisions in complex environments. Here we develop and describe a framework for intelligent data acquisition and real-time database searching and showcase selected examples. The intelligent agent is implemented in the MaxQuant computational proteomics environment, termed MaxQuant Real-Time. It analyzes data as it is acquired on the mass spectrometer, constructs isotope patterns and SILAC pair information as well as controls MS and tandem MS events based on real-time and prior MS data or external knowledge. Re-implementing a top10 method in the intelligent agent yields similar performance to the data dependent methods running on the mass spectrometer itself. We demonstrate the capabilities of MaxQuant Real-Time by creating a real-time search engine capable of identifying peptides "on-the-fly" within 30 ms, well within the time constraints of a shotgun fragmentation "topN" method. The agent can focus sequencing events onto peptides of specific interest, such as those originating from a specific gene ontology (GO) term, or peptides that are likely modified versions of already identified peptides. Finally, we demonstrate enhanced quantification of SILAC pairs whose ratios were poorly defined in survey spectra. MaxQuant Real-Time is flexible and can be applied to a large number of scenarios that would benefit from intelligent, directed data acquisition. Our framework should be especially useful for new instrument types, such as the quadrupole-Orbitrap, that are currently becoming available.

A Framework for Intelligent Data Acquisition and Real-Time Database Searching for Shotgun Proteomics*

PubMed Central

Graumann, Johannes; Scheltema, Richard A.; Zhang, Yong; Cox, Jürgen; Mann, Matthias

2012-01-01

In the analysis of complex peptide mixtures by MS-based proteomics, many more peptides elute at any given time than can be identified and quantified by the mass spectrometer. This makes it desirable to optimally allocate peptide sequencing and narrow mass range quantification events. In computer science, intelligent agents are frequently used to make autonomous decisions in complex environments. Here we develop and describe a framework for intelligent data acquisition and real-time database searching and showcase selected examples. The intelligent agent is implemented in the MaxQuant computational proteomics environment, termed MaxQuant Real-Time. It analyzes data as it is acquired on the mass spectrometer, constructs isotope patterns and SILAC pair information as well as controls MS and tandem MS events based on real-time and prior MS data or external knowledge. Re-implementing a top10 method in the intelligent agent yields similar performance to the data dependent methods running on the mass spectrometer itself. We demonstrate the capabilities of MaxQuant Real-Time by creating a real-time search engine capable of identifying peptides “on-the-fly” within 30 ms, well within the time constraints of a shotgun fragmentation “topN” method. The agent can focus sequencing events onto peptides of specific interest, such as those originating from a specific gene ontology (GO) term, or peptides that are likely modified versions of already identified peptides. Finally, we demonstrate enhanced quantification of SILAC pairs whose ratios were poorly defined in survey spectra. MaxQuant Real-Time is flexible and can be applied to a large number of scenarios that would benefit from intelligent, directed data acquisition. Our framework should be especially useful for new instrument types, such as the quadrupole-Orbitrap, that are currently becoming available. PMID:22171319

Real-time Seismicity Evaluation as a Tool for the Earthquake and Tsunami Short-Term Hazard Assessment (Invited)

NASA Astrophysics Data System (ADS)

Papadopoulos, G. A.

2010-12-01

Seismic activity is a 3-D process varying in the space-time-magnitude domains. When in a target area the short-term activity deviates significantly from the usual (background) seismicity, then the modes of activity may include swarms, temporary quiescence, foreshock-mainshock-aftershock sequences, doublets and multiplets. This implies that making decision for civil protection purposes requires short-term seismic hazard assessment and evaluation. When a sizable earthquake takes place the critical question is about the nature of the event: mainshock or a foreshock which foreshadows the occurrence of a biger one? Also, the seismicity increase or decrease in a target area may signify either precursory changes or just transient seismicity variations (e.g. swarms) which do not conclude with a strong earthquake. Therefore, the real-time seismicity evaluation is the backbone of the short-term hazard assessment. The algorithm FORMA (Foreshock-Mainshock-Aftershock) is presented which detects and updates automatically and in near real-time significant variations of the seismicity according to the earthquake data flow from the monitoring center. The detection of seismicity variations is based on an expert system which for a given target area indicates the mode of seismicity from the variation of two parameters: the seismicity rate, r, and the b-value of the magnitude-frequency relation. Alert levels are produced according to the significance levels of the changes of r and b. The good performance of FORMA was verified retrospectively in several earthquake cases, e.g. for the L’ Aquila, Italy, 2009 earthquake sequence (Mmax 6.3) (Papadopoulos et al., 2010). Real-time testing was executed during January 2010 with the strong earthquake activity (Mmax 5.6) in the Corinth Rift, Central Greece. Evaluation outputs were publicly documented on a nearly daily basis with successful results. Evaluation of coastal and submarine earthquake activity is also of crucial importance for the

First metatarsal closing base wedge osteotomy using real-time fluoroscopy.

PubMed

Toepp, F C; Salcedo, M

1991-01-01

A minimal incision surgery approach to metatarsus primus adductus is presented. The percutaneous closing base wedge osteotomy is performed using real-time intraoperative fluoroscopy. The advantages and disadvantages of this minimal incision surgical procedure are discussed.

Duplex detection of the Mycobacterium tuberculosis complex and medically important non-tuberculosis mycobacteria by real-time PCR based on the rnpB gene.

PubMed

Abdeldaim, Guma; Svensson, Erik; Blomberg, Jonas; Herrmann, Björn

2016-11-01

A duplex real-time PCR based on the rnpB gene was developed for Mycobacterium spp. The assay was specific for the Mycobacterium tuberculosis complex (MTB) and also detected all 19 tested species of non-tuberculous mycobacteria (NTM). The assay was evaluated on 404 clinical samples: 290 respiratory samples and 114 from tissue and other non-respiratory body sites. M. tuberculosis was detected by culture in 40 samples and in 30 samples by the assay. The MTB assay showed a sensitivity similar to Roche Cobas Amplicor MTB-PCR (Roche Molecular Systems, Pleasanton, CA, USA). There were only nine samples with non-tuberculous mycobacteria detected by culture. Six of them were detected by the PCR assay. © 2016 APMIS. Published by John Wiley & Sons Ltd.

Design of a real-time and continua-based framework for care guideline recommendations.

PubMed

Lin, Yu-Feng; Shie, Hsin-Han; Yang, Yi-Ching; Tseng, Vincent S

2014-04-16

Telehealth is an important issue in the medical and healthcare domains. Although a number of systems have been developed to meet the demands of emerging telehealth services, the following problems still remain to be addressed: (1) most systems do not monitor/predict the vital signs states so that they are able to send alarms to caregivers in real-time; (2) most systems do not focus on reducing the amount of work that caregivers need to do, and provide patients with remote care; and (3) most systems do not recommend guidelines for caregivers. This study thus proposes a framework for a real-time and Continua-based Care Guideline Recommendation System (Cagurs) which utilizes mobile device platforms to provide caregivers of chronic patients with real-time care guideline recommendations, and that enables vital signs data to be transmitted between different devices automatically, using the Continua standard. Moreover, the proposed system adopts the episode mining approach to monitor/predict anomalous conditions of patients, and then offers related recommended care guidelines to caregivers so that they can offer preventive care in a timely manner.

Design of a Real-Time and Continua-Based Framework for Care Guideline Recommendations

PubMed Central

Lin, Yu-Feng; Shie, Hsin-Han; Yang, Yi-Ching; Tseng, Vincent S.

2014-01-01

Telehealth is an important issue in the medical and healthcare domains. Although a number of systems have been developed to meet the demands of emerging telehealth services, the following problems still remain to be addressed: (1) most systems do not monitor/predict the vital signs states so that they are able to send alarms to caregivers in real-time; (2) most systems do not focus on reducing the amount of work that caregivers need to do, and provide patients with remote care; and (3) most systems do not recommend guidelines for caregivers. This study thus proposes a framework for a real-time and Continua-based Care Guideline Recommendation System (Cagurs) which utilizes mobile device platforms to provide caregivers of chronic patients with real-time care guideline recommendations, and that enables vital signs data to be transmitted between different devices automatically, using the Continua standard. Moreover, the proposed system adopts the episode mining approach to monitor/predict anomalous conditions of patients, and then offers related recommended care guidelines to caregivers so that they can offer preventive care in a timely manner. PMID:24743843

On irregularities of distribution of real sequences

PubMed Central

Chung, F. R. K.; Graham, R. L.

1981-01-01

A natural measure of the amount of unavoidable clustering that must occur in any bounded infinite sequence of real numbers is studied. We determine the extreme value for this measure and exhibit sequences that achieve this value. PMID:16593046

HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes.

PubMed

Rhee, Soo-Yon; Kantor, Rami; Katzenstein, David A; Camacho, Ricardo; Morris, Lynn; Sirivichayakul, Sunee; Jorgensen, Louise; Brigido, Luis F; Schapiro, Jonathan M; Shafer, Robert W

2006-03-21

HIVseq was developed in 2000 to make published data on the frequency of HIV-1 group M protease and reverse transcriptase (RT) mutations available in real time to laboratories and researchers sequencing these genes. Because most published protease and RT sequences belonged to subtype B, the initial version of HIVseq was based on this subtype. As additional non-B sequences from persons with well-characterized antiretroviral treatment histories have become available, the program has been extended to subtypes A, C, D, F, G, CRF01, and CRF02. The latest frequency of each protease and RT mutation according to subtype and drug-class exposure was calculated using published sequences in the Stanford HIV RT and Protease Sequence Database. Each mutation was hyperlinked to published reports of viruses containing the mutation. As of September 2005, the mean number of protease sequences per non-B subtype was 534 from protease inhibitor-naive persons and 133 from protease inhibitor-treated persons, representing 13.2% and 2.3%, respectively, of the data available for subtype B. The mean number of RT sequences per non-B subtype was 373 from RT inhibitor-naive persons and 288 from RT inhibitor-treated persons, representing 17.9% and 3.8%, respectively, of the data available for subtype B. HIVseq allows users to examine protease and RT mutations within the context of previously published sequences of these genes. The publication of additional non-B protease and RT sequences from persons with well-characterized treatment histories, however, will be required to perform the same types of analysis possible with the much larger number of subtype B sequences.

Real-Time Systems

DTIC Science & Technology

1992-02-01

Postgraduate School Autonomous Under Vehicle (AUV) are then examined. Autonomous underwater vehicle (AUV), hard real-time system, real - time operating system , real-time programming language, real-time system, soft real-time system.

Integration of domain and resource-based reasoning for real-time control in dynamic environments

NASA Technical Reports Server (NTRS)

Morgan, Keith; Whitebread, Kenneth R.; Kendus, Michael; Cromarty, Andrew S.

1993-01-01

A real-time software controller that successfully integrates domain-based and resource-based control reasoning to perform task execution in a dynamically changing environment is described. The design of the controller is based on the concept of partitioning the process to be controlled into a set of tasks, each of which achieves some process goal. It is assumed that, in general, there are multiple ways (tasks) to achieve a goal. The controller dynamically determines current goals and their current criticality, choosing and scheduling tasks to achieve those goals in the time available. It incorporates rule-based goal reasoning, a TMS-based criticality propagation mechanism, and a real-time scheduler. The controller has been used to build a knowledge-based situation assessment system that formed a major component of a real-time, distributed, cooperative problem solving system built under DARPA contract. It is also being employed in other applications now in progress.

Design and application of a web-based real-time personal PM2.5 exposure monitoring system.

PubMed

Sun, Qinghua; Zhuang, Jia; Du, Yanjun; Xu, Dandan; Li, Tiantian

2018-06-15

Growing demand from public health research for conduct large-scale epidemiological studies to explore health effect of PM 2.5 was well-documented. To address this need, we design a web-based real-time personal PM 2.5 exposure monitoring system (RPPM2.5 system) which can help researcher to get big data of personal PM 2.5 exposure with low-cost, low labor requirement, and low operating technical requirements. RPPM2.5 system can provide relative accurate real-time personal exposure data for individuals, researches, and decision maker. And this system has been used in a survey of PM 2.5 personal exposure level conducted in 5 cities of China and has provided mass of valuable data for epidemiological research. Copyright © 2018 Elsevier B.V. All rights reserved.

Microcontroller-based real-time QRS detection.

PubMed

Sun, Y; Suppappola, S; Wrublewski, T A

1992-01-01

The authors describe the design of a system for real-time detection of QRS complexes in the electrocardiogram based on a single-chip microcontroller (Motorola 68HC811). A systematic analysis of the instrumentation requirements for QRS detection and of the various design techniques is also given. Detection algorithms using different nonlinear transforms for the enhancement of QRS complexes are evaluated by using the ECG database of the American Heart Association. The results show that the nonlinear transform involving multiplication of three adjacent, sign-consistent differences in the time domain gives a good performance and a quick response. When implemented with an appropriate sampling rate, this algorithm is also capable of rejecting pacemaker spikes. The eight-bit single-chip microcontroller provides sufficient throughput and shows a satisfactory performance. Implementation of multiple detection algorithms in the same system improves flexibility and reliability. The low chip count in the design also favors maintainability and cost-effectiveness.

Lab-on-a-chip enabled HLA diagnostic: combined sample preparation and real time PCR for HLA-B57 diagnosis

NASA Astrophysics Data System (ADS)

Gärtner, Claudia; Becker, Holger; Hlawatsch, Nadine; Klemm, Richard; Moche, Christian; Schattschneider, Sebastian; Frank, Rainer; Willems, Andreas

2015-05-01

The diverse human HLA (human leukocyte antigen) system is responsible for antigen presentation and recognition. It is essential for the immune system to maintain a stable defense line, but also is also involved in autoimmunity as well as metabolic disease. HLA-haplotype (HLA-B27), for instance, is associated with inflammatory diseases such as Bechterew's disease. The administration of the HIV drug Abacavir in combination with another HLA-haplotype (HLAB57) is associated with severe hypersensitivity reactions. Accordingly, the HLA status has to be monitored for diagnosis or prior to start of therapy. Along this line, a miniaturized microfluidic platform has been developed allowing performing the complete analytical process from "sample-in" to "answer-out" in a point-of-care environment. The main steps of the analytical cascade inside the integrated system are blood cell lysis and DNA isolation, DNA purification, real-time PCR and quantitative monitoring of the rise of a fluorescent signal appearing during the PCR based sequence amplification. All bio-analytical steps were intended to be performed inside one chip and will be actuated, controlled and monitored by a matching device. This report will show that all required processes are established and tested and all device components work well and interact with the functional modules on the chips in a harmonized fashion.

Routine HLA-B genotyping with PCR-sequence-specific oligonucleotides detects a B*52 variant (B*5206).

PubMed

Hoelsch, K; Lenggeler, I; Pfannes, W; Knabe, H; Klein, H-G; Woelpl, A

2005-05-01

A new human leukocyte antigen (HLA)-B allele was found during routine typing of samples for a German unrelated bone marrow donor registry, the "Aktion Knochenmarkspende Bayern". After first interpretation of data of two independent low-resolution sequence-specific oligonucleotide typing tests, a B*51 variant was suggested. Further analysis via sequence-based typing identified the sequence as new B*52 allele. This new allele officially assigned as B*5206 differs from HLA-B*520102 by one nucleotide exchange in exon 2. The mutation is located at nucleotide position 274, at which a cytosine is substituted by a thymine leading to an amino acid change at protein position 67 from serine (TCC) to phenylalanine (TTC).

The Power of Real-Time PCR

ERIC Educational Resources Information Center

Valasek, Mark A.; Repa, Joyce J.

2005-01-01

In recent years, real-time polymerase chain reaction (PCR) has emerged as a robust and widely used methodology for biological investigation because it can detect and quantify very small amounts of specific nucleic acid sequences. As a research tool, a major application of this technology is the rapid and accurate assessment of changes in gene…

1/32° real-time global ocean prediction and value-added over 1/16° resolution

NASA Astrophysics Data System (ADS)

Shriver, J. F.; Hurlburt, H. E.; Smedstad, O. M.; Wallcraft, A. J.; Rhodes, R. C.

2007-03-01

A 1/32° global ocean nowcast/forecast system has been developed by the Naval Research Laboratory at the Stennis Space Center. It started running at the Naval Oceanographic Office in near real-time on 1 Nov. 2003 and has been running daily in real-time since 1 Mar. 2005. It became an operational system on 6 March 2006, replacing the existing 1/16° system which ceased operation on 12 March 2006. Both systems use the NRL Layered Ocean Model (NLOM) with assimilation of sea surface height from satellite altimeters and sea surface temperature from multi-channel satellite infrared radiometers. Real-time and archived results are available online at http://www.ocean.nrlssc.navy.mil/global_nlom. The 1/32° system has improvements over the earlier system that can be grouped into two categories: (1) better resolution and representation of dynamical processes and (2) design modifications. The design modifications are the result of accrued knowledge since the development of the earlier 1/16° system. The improved horizontal resolution of the 1/32° system has significant dynamical benefits which increase the ability of the model to accurately nowcast and skillfully forecast. At the finer resolution, current pathways and their transports become more accurate, the sea surface height (SSH) variability increases and becomes more realistic and even the global ocean circulation experiences some changes (including inter-basin exchange). These improvements make the 1/32° system a better dynamical interpolator of assimilated satellite altimeter track data, using a one-day model forecast as the first guess. The result is quantitatively more accurate nowcasts, as is illustrated by several model-data comparisons. Based on comparisons with ocean color imagery in the northwestern Arabian Sea and the Gulf of Oman, the 1/32° system has even demonstrated the ability to map small eddies, 25-75 km in diameter, with 70% reliability and a median eddy center location error of 22.5 km, a